Methods of treating viral infections using inhibitors of nucleotide synthesis pathways

ABSTRACT

The invention provided methods of treating viral infections, such as COVID-19, by providing an agent that inhibits a nucleotide synthesis pathway. In certain methods, the agent is an inhibitor of dihydroorotate dehydrogenase, such as a brequinar. In certain methods, brequinar is provided to a subject according to a dosing regimen that tailors levels of the drug in the lungs to achieve optimal therapeutic benefit. The dosing regimen may include defined levels of brequinar administered to the subject or defined levels of brequinar attained the lungs of the subject. The invention also provides combination therapies in which an inhibitor of dihydroorotate dehydrogenase is provided together with a second therapeutic agent.

FIELD OF THE INVENTION

The invention relates generally to methods of treating viral infections.

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic is the most devastating global epidemic of infectious disease in over a century. Within six months after COVID-19 was first identified, the disease had afflicted more than 6 million people and killed nearly 400,000 worldwide. The rapid spread of COVID-19 led most developed countries to impose severe social-distancing measures that require individuals to avoid coming into proximity with each other except to perform essential activities. Consequently, the COVID-19 pandemic has also disrupted the social and economic lives of communities across the globe.

COVID-19 is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 infects epithelial cells of the respiratory tract, and the lungs are the organs most affected by the virus. The symptoms of mild cases of COVID-19 include coughing, shortness of breath, fatigue, and fever. However, many patients with COVID-19 develop acute respiratory distress syndrome, which may be fatal or permanently debilitating. Transmission of SARS-CoV-2 occurs predominantly via droplets that result from coughing or talking, so the virus spreads easily among individuals in physical proximity. Currently, there is no vaccine for SARS-CoV-2.

SUMMARY

The invention provides methods of treating viral infections, such as COVID-19, by providing one or more agents that suppress viral replication by inhibiting a nucleotide synthesis pathway in cells of the subject. Viruses require an abundant supply of nucleotides to reproduce within cells, and nucleotide starvation thwarts viral replication. The invention provides methods of depleting nucleotide pools using inhibitors of dihydroorotate dehydrogenase (DHODH), such as brequinar, which block synthesis of pyrimidine-based nucleotides. Inhibitors of pyrimidine synthesis may be used alone or in combination with other classes of drugs, such as inhibitors of purine synthesis or other antiviral drugs.

The invention also provides methods of treating respiratory viral infections by providing brequinar or a pharmaceutically acceptable salt thereof to a subject according to a dosing regimen that tailors levels of the drug in the lungs to achieve optimal therapeutic benefit. The invention recognizes that sustained periods of nucleotide starvation are necessary to suppress viral replication. Methods of the invention include dosing regimens that maintain levels of brequinar in the lungs at high enough concentrations for long enough periods to prevent viral replication without harming the body's own cells. The dosing regimens may also include dosage-free periods that allow replenishment of nucleotide pools to support normal cellular processes. Because the dosing regimens of the invention deliver brequinar the lungs in defined amounts for defined periods, they are useful for treating infections with any virus, such as SARS-CoV-2, that targets the respiratory system.

In an aspect, the invention provides methods of treating a viral infection by providing to a subject having a viral infection an agent that inhibits a nucleotide synthesis pathway in cells of the subject, thereby reducing, suppressing, or inhibiting viral replication.

The viral infection may be a respiratory viral infection. The virus may infect a particular tissue within the respiratory system. The virus may infect one or more of the alveoli, bronchi, bronchioles, larynx, lungs, nasal cavities, nose, pharynx, respiratory system, sinuses, and trachea.

The respiratory viral infection may include any virus that infects the respiratory system. The respiratory virus may be an adenovirus, coronavirus, human metapneumovirus, human parainfluenza virus, human respiratory syncytial virus, influenza virus, or rhinovirus. The coronavirus may be Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The influenza virus may be influenza A, influenza B, influenza C, or influenza D. The influenza A virus may be a H1N1, H3N2, N9N2, or H5N1 strain.

The agent may inhibit pyrimidine synthesis. The agent may be a dihydroorotate dehydrogenase (DHODH) inhibitor. The DHODH inhibitor may be brequinar, a brequinar analog, a brequinar derivative, a brequinar prodrug, a micellar formulation of brequinar, a brequinar hydrate, or a brequinar salt. The brequinar salt may be a sodium salt. The DHODH inhibitor may be leflunomide or teriflunomide.

The method may include providing to the subject an antiviral agent. The antiviral agent may be a direct-acting antiviral agent. The antiviral agent may be a 3C-like main protease inhibitor, eIF4E inhibitor, helicase inhibitor, inhibitor or a viral protein that binds to a host receptor, inhibitor of a viral structural protein, inhibitor of a virulence factor, inosine monophosphate dehydrogenase (IMPDH) inhibitor, interferon, papain-like proteinase inhibitor, protease inhibitor, RNA-dependent RNA polymerase inhibitor, or xanthine oxidase inhibitor.

The 3C-like main protease inhibitor may be (1S,2R,4aS,5R,8aS)-1-formamido-1,4a-dimethyl-6-methylene-5-((E)-2-(2-oxo-2,5-dihydrofuran-3-yl)ethenyl)decahydronaphthalen-2-yl 5-((R)-1,2-dithiolan-3-yl) pentanoate, (1S,2R,4aS,5R,8aS)-1-formamido-1,4a-dimethyl-6-methylene-5-((E)-2-(2-oxo-2,5-dihydrofuran-3-yl)ethenyl)decahydronaphthalen-2-yl 2-nitrobenzoate, (S)-(1S,2R,4aS,5R,8aS)-1-formamido-1,4a-dimethyl-6-methylene-5-((E)-2-(2-oxo-2,5-dihydrofuran-3-yl)ethenyl)decahydronaphthalen-2-yl-2-amino-3-phenylpropanoate, 2-((1R,5R,6R,8aS)-6-Hydroxy-5-(hydroxymethyl)-5,8a-dimethyl-2-methylenedecahydronaphthalen-1-yl)ethyl benzoate, 2β-Hydroxy-3, 4-seco-friedelolactone-27-oic acid, alfuzosin, almitrine, amprenavir, andrograpanin, andrographiside, betulonal, carminic acid, carvedilol, cefpiramide, cerevisterol, chlorhexidine, chrysin-7-O-β-glucuronide, cilastatin, cosmosiin, demeclocycline, famotidine, flavin mononucleotide, hesperidin, isodecortinol, lutein, lymecycline, mimosine, montelukast, neohesperidin, nepafenac, phenethicillin, progabide, or tigecycline.

The eIF4E inhibitor may be ribavirin.

The IMPDH inhibitor may be AS2643361, EICAR, FF-10501, mizoribine, mycophenolic acid, mycophenolate mofetil, ribavirin, selenazofurin, SM-108, taribavirin, tiazofurin, VX-148, VX-497, or VX-944.

The interferon may be peginterferon alpha-2a or peginterferon alpha-2b.

The papain-like proteinase inhibitor may be (−)-epigallocatechin gallate, (S)-(1S,2R,4aS,5R,8aS)-1-formamido-1,4a-dimethyl-6-methylene-5-((E)-2-(2-oxo-2,5-dihydrofuran-3-yl)ethenyl) decahydronaphthalen-2-yl-2-amino-3-phenylpropanoate, 2-(3,4-dihydroxyphenyl)-2-[[2-(3,4-dihydroxyphenyl)-3,4-dihydro-5,7-dihydroxy-2H-1-benzopyran-3-yl]oxy]-3,4-dihydro-2H-1-benzopyran-3,4,5,7-tetrol, 2,20-cyclocytidine, 2,2-di (3-indolyl)-3-indolone, acetophenazine, ademetionine, aspartame, baicalin, cefamandole, chloramphenicol, chlorphenesin carbamate, chrysin, dantrolene, doxycycline, floxuridine, glutathione, hesperetin, iopromide, isotretinoin, L(+)-ascorbic acid, levodropropizine, magnolol, masoprocol, neohesperidin, nicardipine, oxprenolol, pemetrexed, phaitanthrin D, piceatannol, platycodin D, reproterol, ribavirin, riboflavin, rosmarinic acid, sildenafil, silybin, sugetriol-3,9-diacetate, sulfasalazine, tigecycline, valganciclovir, or β-thymidine.

The protease inhibitor may be lopinavir, ritonavir, or a combination thereof.

The RNA-dependent RNA polymerase inhibitor may be (R)-((1R,5aS,6R,9aS)-1,5a-dimethyl-7-methylene-3-oxo-6-((E)-2-(2-oxo-2,5-dihydrofuran-3-yl)ethenyl)decahydro-1H-benzo[c]azepin-1-yl)methyl 2-amino-3-phenylpropanoate, 14-deoxy-11,12-didehydroandrographolide, 14-hydroxycyperotundone, 2-((1R,5R,6R,8aS)-6-hydroxy-5-(hydroxymethyl)-5,8a-dimethyl-2-methylenedecahydronaphthalen-1-yl)ethyl benzoate, 2-(3,4-dihydroxyphenyl)-2-[[2-(3,4-dihydroxyphenyl)-3,4-dihydro-5,7-dihydroxy-2H-1-benzopyran-3-yl]oxy]-3,4-dihydro-2H-1-benzopyran-3,4,5,7-tetrol, 20,300-dihydroxy-3,4-seco-friedelolactone-27-lactone, 20-hydroxy-3, 4-seco-friedelolactone-27-oic acid, andrographiside, AT-511, AT-527, AT-9010, atovaquone, beclabuvir, benzylpenicilloyl G, betulonal, bromocriptine, ceftibuten, cefuroxime, chenodeoxycholic acid, chlorhexidine, cortisone, cromolyn, dabigatran etexilate, dasabuvir, deleobuvir, diphenoxylate, favipiravir, fenoterol, filibuvir, fludarabine, galidesivir, gnidicin, gniditrin, idarubicin, itraconazole, novobiocin, pancuronium bromide, penciclovir, phyllaemblicin B, ponatinib, radalbuvir, remdesivir, setrobuvir, silybin, sofosbuvir, sugetriol-3,9-diacetate, theaflavin 3,30-di-O-gallate, tegobuvir, tibolone, or valganciclovir,

The virulence factor may be Nsp1, Nsp3c, or ORF7a.

The xanthine oxidase inhibitor may be allopurinol, oxypurinol, tisopurine, topiroxostat, phytic acid, or myoinositol.

The antiviral agent may target 3CLpro, ACE2, C-terminal RNA binding domain (CRBD), E-channel (E protein), helicase, RNA-dependent RNA polymerase, and Nsp1, Nsp3 (including one or more of Nsp3b, Nsp3c, PLpro, and Nsp3e), Nsp7-Nsp8 complex, Nsp9-Nsp10, and Nsp14-Nsp16, N-terminal RNA binding domain (NRBD), ORF7a, Spike, or TMPRSSS2.

The method may include providing to the subject an agent that inhibits purine synthesis. The purine synthesis inhibitor may be an inosine monophosphate dehydrogenase (IMPDH) inhibitor. The IMPDH inhibitor may be ribavirin, mycophenolate mofetil, or mycophenolate. Mycophenolate mofetil or mycophenolate may be provided in conjunction with allopurinol.

Each agent may independently be provided orally, intravenously, enterally, parenterally, dermally, buccally, topically, transdermally, by injection, subcutaneously, nasally, pulmonarily, or with or on an implantable medical device.

The agent that inhibits a nucleotide synthesis pathway and the second agent may be provided in the same formulation. The agent that inhibits a nucleotide synthesis pathway and the second agent may be provided in separate formulations.

In another aspect, the invention provides methods of treating a viral infection by providing to a subject having a viral infection a combination that includes an agent that inhibits pyrimidine synthesis in cells of the subject and an agent that inhibits purine synthesis in cells of the subject, thereby reducing, suppressing, or inhibiting viral replication.

The viral infection may a be respiratory infection. The respiratory viral infection may include any of the viruses described above.

The agent inhibits pyrimidine synthesis may be a DHODH inhibitor, such as any of those described above.

The agent inhibits purine synthesis may be an IMPDH inhibitor, such as any of those described above.

The combination may be or include one the following: brequinar and ribavirin; brequinar and mycophenolate; leflunomide and mycophenolate; teriflunomide and ribavirin; and teriflunomide and mycophenolate. The combinations may also include allopurinol. Each of the above agents may be provided as a pharmaceutically acceptable salt thereof.

The agent that inhibits pyrimidine synthesis and the agent that inhibits purine synthesis may be provided in the same formulation. The agent that inhibits pyrimidine synthesis and the agent that inhibits purine synthesis may be provided in separate formulations.

In another aspect, the invention provides methods of treating a viral infection by providing to a subject having a viral infection a combination that includes an agent that inhibits a nucleotide synthesis pathway in cells of the subject and an antiviral agent, thereby reducing, suppressing, or inhibiting viral replication.

The antiviral agent may be any of those described above.

The viral infection may a respiratory infection. The respiratory viral infection may include any of the viruses described above.

The combination may be or include one the following: brequinar and ribavirin; brequinar and remdesivir; brequinar, lopinavir, and ritonavir; brequinar and favipiravir; and brequinar, ribavirin, lopinavir, and ritonavir. Each of the above agents may be provided as a pharmaceutically acceptable salt thereof.

The agent that inhibits a nucleotide synthesis pathway and the antiviral agent may be provided in the same formulation. The agent that inhibits a nucleotide synthesis pathway and the antiviral agent may be provided in separate formulations.

In another aspect, the invention provides methods of treating or preventing a viral infection in a subject that has been exposed to a virus by providing to a subject that has been exposed to a virus an agent that inhibits a nucleotide synthesis pathway in cells of the subject, thereby reducing, suppressing, or inhibiting viral replication in the subject.

The virus may be respiratory virus, such as any of those described above.

The agent may inhibit pyrimidine synthesis. The agent may be a dihydroorotate dehydrogenase (DHODH) inhibitor, such as any of those described above.

The agent may be brequinar or a pharmaceutically acceptable salt thereof. Brequinar or a pharmaceutically acceptable salt thereof may be provided according to a dosing regimen that includes at least one dosage of from about 10 mg to about 4000 mg of brequinar per 24-hour period. The dosage may be from about 10 mg to about 4000 mg, from about 26 mg to about 4000 mg, from about 51 mg to about 4000 mg, from about 76 mg to about 4000 mg, from about 101 mg to about 4000 mg, from about 151 mg to about 4000 mg, from about 201 mg to about 4000 mg, from about 10 mg to about 2000 mg, from about 26 mg to about 2000 mg, from about 51 mg to about 2000 mg, from about 76 mg to about 2000 mg, from about 101 mg to about 2000 mg, from about 151 mg to about 2000 mg, from about 201 mg to about 2000 mg, from about 10 mg to about 1000 mg, from about 26 mg to about 1000 mg, from about 51 mg to about 1000 mg, from about 76 mg to about 1000 mg, from about 101 mg to about 1000 mg, from about 151 mg to about 1000 mg, from about 201 mg to about 1000 mg, from about 10 mg to about 500 mg, from about 26 mg to about 500 mg, from about 51 mg to about 500 mg, from about 76 mg to about 500 mg, from about 101 mg to about 500 mg, from about 151 mg to about 500 mg, from about 201 mg to about 500 mg, from about 10 mg to about 300 mg, from about 26 mg to about 300 mg, from about 51 mg to about 300 mg, from about 76 mg to about 300 mg, from about 101 mg to about 300 mg, from about 151 mg to about 300 mg, from about 201 mg to about 300 mg, from about 10 mg to about 200 mg, from about 26 mg to about 200 mg, from about 51 mg to about 200 mg, from about 76 mg to about 200 mg, from about 101 mg to about 200 mg, from about 151 mg to about 200 mg, from about 10 mg to about 150 mg, from about 26 mg to about 150 mg, from about 51 mg to about 150 mg, from about 76 mg to about 150 mg, from about 101 mg to about 150 mg, from about 10 mg to about 100 mg, from about 26 mg to about 100 mg, from about 51 mg to about 100 mg, from about 76 mg to about 100 mg, about 50 mg, about 75 mg, about 100 mg, about 200 mg, about 250 mg, about 300 mg, about 400 mg, about 500 mg, about 1000 mg, about 2000 mg, or about 4000 mg.

The dosing regimen may include multiple dosages provided in consecutive 24-hour periods. The dosing regimen may include 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 dosages provided in consecutive 24-hour periods.

The dosing regimen may include multiple dosages that are the same. The dosing regimen may include multiple dosages that are not all the same. The dosing regimen may include a first dosage that is higher than subsequent dosages. The dosing regimen may include a first two, three, or four dosages that are higher than subsequent dosages. The dosage may include a first dosage that is lower than subsequent dosages. The dosing regimen may include a first two, three, or four dosages that are higher than subsequent dosages. Each dosage may independently be any of the dosages described above. For example, the first dosage may be 100 mg, and the subsequent dosages may be 25 mg, 50 mg, or 75 mg.

The dosing regimen may include a dosage-free period in which the subject does not receive brequinar or a pharmaceutically acceptable salt thereof. The dosage-free period may be at least 12 hours, at least 24 hours, at least 36 hours, at least 48 hours, at least 60 hours, at least 72 hours, at least 5 days, at least 7 days, at least 10 days, at least 14 days, about 12 hours, about 24 hours, about 36 hours, about 48 hours, about 60 hours, about 72 hours, about 5 days, about 7 days, about 10 days, or about 14 days.

The dosage-free period may follow a dosage. The dosage-free period may follow multiple dosages provided over consecutive 24-hour periods. The dosage-free period may follow multiple dosages provided over 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 consecutive 24-hour periods. The dosage-free period may occur directly after the last of the consecutive dosages.

The dosage may include a single dose. The dosage may include multiple doses. The dosage may include 2, 3, 4, 6, or 8 doses.

In another aspect, the invention provides methods of treating or preventing a viral infection in a subject by providing to a subject, prior to exposure of the subject to a virus, an agent that inhibits a nucleotide synthesis pathway in cells of the subject, thereby reducing, suppressing, or inhibiting viral replication in the subject.

The virus may be respiratory virus, such as any of those described above.

The agent may inhibit pyrimidine synthesis. The agent may be a dihydroorotate dehydrogenase (DHODH) inhibitor, such as any of those described above.

The agent may be brequinar or a pharmaceutically acceptable salt thereof. Brequinar or a pharmaceutically acceptable salt thereof may be provided according to a dosing regimen that includes at least one dosage of from about 10 mg to about 4000 mg of brequinar per 24-hour period. The dosage may be any of those described above.

The dosing regimen may include multiple dosages provided in consecutive 24-hour periods. The dosing regimen may include 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 dosages provided in consecutive 24-hour periods.

The dosing regimen may include multiple dosages that are the same. The dosing regimen may include multiple dosages that are not all the same. The dosing regimen may include a first dosage that is higher than subsequent dosages. The dosing regimen may include a first two, three, or four dosages that are higher than subsequent dosages. The dosage may include a first dosage that is lower than subsequent dosages. The dosing regimen may include a first two, three, or four dosages that are higher than subsequent dosages. Each dosage may independently be any of the dosages described above. For example, the first dosage may be 100 mg, and the subsequent dosages may be 25 mg, 50 mg, or 75 mg.

The dosing regimen may include a dosage-free period in which the subject does not receive brequinar or a pharmaceutically acceptable salt thereof. The dosage-free period may be any of those described above.

The dosage-free period may follow a dosage. The dosage-free period may follow multiple dosages provided over consecutive 24-hour periods. The dosage-free period may follow multiple dosages provided over 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 consecutive 24-hour periods. The dosage-free period may occur directly after the last of the consecutive dosages.

In another aspect, the invention provides methods of treating a respiratory viral infection in a subject by providing brequinar or a pharmaceutically acceptable salt thereof to a subject having a respiratory viral infection according to a dosing regimen that includes at least one dosage of from about 10 mg to about 180 mg of brequinar per 24-hour period.

The dosage may be from about 10 mg to about 180 mg, from about 26 mg to about 180 mg, from about 51 mg to about 180 mg, from about 76 mg to about 180 mg, from about 101 mg to about 180 mg, from about 126 mg to about 180 mg, from about 151 mg to about 180 mg, from about 10 mg to about 150 mg, from about 26 mg to about 150 mg, from about 51 mg to about 150 mg, from about 76 mg to about 150 mg, from about 101 mg to about 150 mg, from about 126 mg to about 150 mg, from about 10 mg to about 125 mg, from about 26 mg to about 125 mg, from about 51 mg to about 125 mg, from about 76 mg to about 125 mg, from about 101 mg to about 125 mg, from about 10 mg to about 100 mg, from about 26 mg to about 100 mg, from about 51 mg to about 100 mg, from about 76 mg to about 100 mg, from about 10 mg to about 75 mg, from about 26 mg to about 75 mg, from about 51 mg to about 75 mg, from about 10 mg to about 50 mg, from about 26 mg to about 50 mg, about 10 mg, about 25 mg, about 50 mg, about 75 mg, about 100 mg, about 125 mg, about 150 mg, or about 180 mg.

The dosing regimen may include multiple dosages provided in consecutive 24-hour periods. The dosing regimen may include 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 dosages provided in consecutive 24-hour periods.

The dosing regimen may include multiple dosages that are the same. The dosing regimen may include multiple dosages that are not all the same. The dosing regimen may include a first dosage that is higher than subsequent dosages. The dosing regimen may include a first two, three, or four dosages that are higher than subsequent dosages. The dosage may include a first dosage that is lower than subsequent dosages. The dosing regimen may include a first two, three, or four dosages that are higher than subsequent dosages. Each dosage may independently be any of the dosages described above. For example, the first dosage may be 100 mg, and the subsequent dosages may be 25 mg, 50 mg, or 75 mg.

The dosing regimen may include a dosage-free period in which the subject does not receive brequinar or a pharmaceutically acceptable salt thereof. The dosage-free period may be at least 12 hours, at least 24 hours, at least 36 hours, at least 48 hours, at least 60 hours, at least 72 hours, at least 5 days, at least 7 days, at least 10 days, at least 14 days, about 12 hours, about 24 hours, about 36 hours, about 48 hours, about 60 hours, about 72 hours, about 5 days, about 7 days, about 10 days, or about 14 days.

The dosage-free period may follow a dosage. The dosage-free period may follow multiple dosages provided over consecutive 24-hour periods. The dosage-free period may follow multiple dosages provided over 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 consecutive 24-hour periods. The dosage-free period may occur directly after the last of the consecutive dosages.

The dosage may include a single dose. The dosage may include multiple doses. The dosage may include 2, 3, 4, 6, or 8 doses.

The respiratory viral infection may include any of the respiratory viruses described above.

The virus may infect a particular part of the respiratory system, such as any of those described above.

The method may include providing an antiviral agent to the subject. The antiviral agent may be any of those described above.

The dosage may be provided orally, intravenously, enterally, parenterally, dermally, buccally, topically, transdermally, by injection, subcutaneously, nasally, pulmonarily, or with or on an implantable medical device.

The brequinar may be provided as a brequinar analog, a brequinar derivative, a brequinar prodrug, a micellar formulation of brequinar, a brequinar hydrate, or a brequinar salt. The brequinar salt may be a sodium salt.

In another aspect, the invention provides methods of treating a respiratory viral infection in a subject by providing brequinar or a pharmaceutically acceptable salt thereof to a subject having a respiratory viral infection according to a dosing regimen that includes at least one dosage sufficient to maintain a concentration of brequinar in a lung of the subject of at least at least 0.375 μg/mL for a 24-hour period.

The dosing regimen may be sufficient to maintain a concentration of brequinar in a lung of the subject of at least 0.4 μg/mL, at least 0.5 μg/mL, at least 0.6 μg/mL, at least 0.8 μg/mL, at least 1 μg/mL, at least 1.5 μg/mL, or at least 2 μg/mL for a 24-hour period.

The dosing regimen may include multiple dosages provided in consecutive 24-hour periods. The dosing regimen may include 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 dosages provided in consecutive 24-hour periods.

The dosing regimen may include multiple dosages that are the same. The dosing regimen may include multiple dosages that are not all the same. The dosing regimen may include a first dosage that is higher than subsequent dosages. The dosing regimen may include a first two, three, or four dosages that are higher than subsequent dosages. The dosage may include a first dosage that is lower than subsequent dosages. The dosing regimen may include a first two, three, or four dosages that are higher than subsequent dosages. Each dosage may independently be any of the dosages described above. For example, the first dosage may be 100 mg, and the subsequent dosages may be 25 mg, 50 mg, or 75 mg.

The dosing regimen may include a dosage-free period in which the subject does not receive brequinar or a pharmaceutically acceptable salt thereof. The dosage-free period may be at least 12 hours, at least 24 hours, at least 36 hours, at least 48 hours, at least 60 hours, at least 72 hours, at least 5 days, at least 7 days, at least 10 days, at least 14 days, about 12 hours, about 24 hours, about 36 hours, about 48 hours, about 60 hours, about 72 hours, about 5 days, about 7 days, about 10 days, or about 14 days.

The dosage-free period may follow a dosage. The dosage-free period may follow multiple dosages provided over consecutive 24-hour periods. The dosage-free period may follow multiple dosages provided over 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 consecutive 24-hour periods. The dosage-free period may occur directly after the last of the consecutive dosages.

The dosage may include a single dose. The dosage may include multiple doses. The dosage may include 2, 3, 4, 6, or 8 doses.

The respiratory viral infection may include any of the respiratory viruses described above.

The virus may infect a particular part of the respiratory system, such as any of those described above.

The method may include providing an antiviral agent to the subject. The antiviral agent may be any of those described above.

The dosage may be provided orally, intravenously, enterally, parenterally, dermally, buccally, topically, transdermally, by injection, subcutaneously, nasally, pulmonarily, or with or on an implantable medical device.

The brequinar may be provided as a brequinar analog, a brequinar derivative, a brequinar prodrug, a micellar formulation of brequinar, a brequinar hydrate, or a brequinar salt. The brequinar salt may be a sodium salt.

In another aspect, the invention includes methods of treating a viral infection in a subject by providing to a subject having a viral infection a combination that includes an agent that inhibits a nucleotide synthesis pathway in cells of the subject and an anti-inflammatory agent.

The agent that inhibits a nucleotide synthesis pathway may inhibit pyrimidine synthesis. The agent may be a dihydroorotate dehydrogenase (DHODH) inhibitor. The DHODH inhibitor may be brequinar, a brequinar analog, a brequinar derivative, a brequinar prodrug, a micellar formulation of brequinar, a brequinar hydrate, or a brequinar salt. The brequinar salt may be a sodium salt. The DHODH inhibitor may be leflunomide or teriflunomide.

The anti-inflammatory agent may be a corticosteroid or non-steroidal anti-inflammatory drug (NSAID). The anti-inflammatory agent may be acematricin, acetate, aloe vera extracts, alpha-methyl dexamethasone, amcinafide, arnica flower, asprin, beclamethasone dipropionate, benorylate, benoxaprofen, betamethasone and its esters, chloroprednisone, chloroprednisone acetate, clescinolone, clidanac, clobetasol valerate, clocortelone, comfrey root, desonide, desoxycorticosterone acetate, desoxymethasone, dexamethasone, dexamethasone phosphate, dichlorisone, dichlorisone, diclofenac, di-florasone diacetate, diflucortolone and its derivatives, difluprednate, disalacid, enolic acids, extracts from genus Commiphom (Commiphora mukul), extracts from genus Rubis (Rubia cordifolia), fenamic acid derivatives, fenclofenac, fenugreek seed, fluadrenolone, flubiprofen, flucloronide, flucortine butyl ester, flucrolone acetonide, flufenamic acid derivatives such as N-(α,α,α-trifluoro-m-tolyl) anthranilic acid), flunisolide, fluocinonide, fluocortolone, fluoromethalone, fluperolone, fluprednidine, fluprednisolone, flurandrenolone, furofenac, halcinonide, hydrocortamate, hydrocortisone, hydrocortisone acetate, hydrocortisone butyrate, hydrocortisone cyclopentylpropionate, hydrocortisone valerate, hydroxytriamcilone, indomethacin, isozepac, ketoprofen, matricarria flowers, meclofenamic acid derivatives (e.g. sodium meclofenamate), medrysone, mefenamic acid derivatives (e.g. N-(2,3-xyl-yl) anthranilic acid), meprednisone, methylprednisolone, naproxen, oxicams (e.g. piroxicam and isoxicam), oxyphenbutazone, paramethasone, phenylbutazone, prednisolone, prednisone, propionic acid esters such as ibuprofen, pyrazolidinediones, such as feprazone, safaprin, salicylic acid derivatives, sulfinpyrazone, sulindac, suprofen, tolmetin, triamcinolone acetonide, trimethasone, trisilate, willow bark, or zomepirac.

The agent that inhibits a nucleotide synthesis pathway may be provided to the subject during a first period, and the anti-inflammatory agent may be provided to the subject during a second period that follows the first period. The agent that inhibits a nucleotide synthesis pathway may not be provided to the subject during the first period. The anti-inflammatory may be provided to the subject during the first period. The anti-inflammatory may not be provided to the subject during the first period.

The agent that inhibits a nucleotide synthesis pathway may be brequinar or a pharmaceutically acceptable salt, and it may be provided to the subject during the first period according to a dosing regimen, such as any of those described above. The dosing regimen may include any of the dosages described above.

The viral infection may a be respiratory infection. The respiratory viral infection may include any of the viruses described above. The agent that inhibits a nucleotide synthesis pathway and the anti-inflammatory agent may be provided in the same formulation. For example, brequinar or a pharmaceutically acceptable salt thereof and dexamethasone may be provided in the same formulation. The agent that inhibits a nucleotide synthesis pathway and the anti-inflammatory agent may be provided in separate formulations. For example, brequinar or a pharmaceutically acceptable salt thereof and dexamethasone may be provided in separate formulations.

Metabolites

The invention provides methods and devices that allow physicians to determine, optionally in real time, a therapeutically effective dose of a drug for an individual patient by examining levels of a metabolite in a pathway targeted by the drug. In particular embodiments, the effectiveness of a drug containing an enzyme inhibitor is assessed by analyzing the level of the enzyme's substrate in a sample obtained from the patient. Because activity of the enzyme can be inferred from substrate levels, engagement of the API with its target can be evaluated, optionally in real time, and drug dosage can be adjusted accordingly. Thus, compared to prior methods that rely on levels of the API or a metabolite of the API to calibrate drug dosage, the methods of the invention yield dosing schedules that afford better control of a variety of diseases, disorders, and conditions and decrease the risk harmful drug side effects. The invention also provides devices that notify patients, in real time, of recommended adjustments to their dosing regimens based on measured levels of a metabolite in the pathway targeted by the drug.

Because the methods permit real-time adjustment of drug dosage to optimize therapeutic effectiveness, they are useful for treatment of various diseases, such as cancer. For example, control of dihydroorotate dehydrogenase (DHODH) in acute myeloid leukemia (AML) could selectively starve leukemia cells, so the DHODH inhibitor brequinar has potential as an anti-cancer agent. However, achieving a therapeutically effective dosing regimen of brequinar is problematic: when the drug is administered frequently, e.g., daily, it causes toxic side effects, and when it is administered too infrequently, e.g., biweekly or on a schedule that requires extended “off” periods between doses, it has no therapeutic benefit. Methods of the invention solve this problem by monitoring levels of dihydroorotate (DHO), the substrate for DHODH, in the patient's body to determine the frequency and dose for administration of brequinar. Consequently, the invention unlocks the therapeutic potential of brequinar and other drugs that have narrow therapeutic windows or high interindividual variability.

The invention also provides methods of evaluating the effectiveness of anti-cancer agents by assessing their effects on tumors, optionally in real time. The methods involve analyzing properties of a tumor in the body, such as the flux or single point level of a nutrient, substrate, or metabolite in the tumor or the level of oxygenation of the tumor. By monitoring these properties in a patient who has been given a therapeutic agent, the impact of the drug on the tumor can be gauged, and the dosing regimen can be adjusted accordingly.

In an aspect, the invention provides methods for determining a therapeutically effective dose of an agent to treat a disorder in a subject. The methods include receiving information regarding a measured level of a metabolite in a metabolic pathway in a sample from a subject having a disorder, comparing the received information to a reference that provides an association of a measured level of the metabolite with a recommended dosage adjustment of an agent, and determining, based on the comparing step, a dosage of the agent that results in the level of the metabolite being raised or maintained above a threshold level. The threshold level is indicative that a sufficient amount of the agent is present in the subject to sufficiently alter the metabolic pathway to ameliorate, reduce, or eliminate at least one sign or symptom of the disorder.

In another aspect, the invention provides methods for determining a therapeutically effective dose of an agent to be provided to a subject to treat a disorder. The methods include determining a therapeutically effective dose of an agent based on a measured level of a metabolite in a nucleotide synthesis pathway in a sample from a subject. The therapeutically effective dose of the agent inhibits an enzyme within the nucleotide synthesis pathway to an extent that at least one sign or symptom of the disorder is ameliorated, reduced, or eliminated.

The recommend dosage adjustment may include a change in the dosage. For example, the recommend dosage adjustment may include an increase of the dosage by a certain value, a decrease of the dosage by a certain value, or no adjustment to the dosage. The recommended dosage adjustment may include a change in the schedule of providing the dose. For example, the recommended dosage adjustment may include an increase in the interval between doses, a decrease in the interval between doses, or no change in the interval between doses.

The agent may be any therapeutic agent. For example, the agent may be PALA (N-phosphoacetyl-L-aspartate), brequinar, pyrazofurin, brequinar, a brequinar analog, a brequinar derivative, a brequinar prodrug, a micellar formulation of brequinar, or a brequinar salt. The agent may inhibit an enzyme in the metabolic pathway. For example, the agent may inhibit aspartate transcarbamoylase, dihydrooratase, dihydroorotate dehydrogenase, orotidine 5′-monophosphate (OMP) decarboxylase, or orotate phosphoribosyl transferase.

The metabolite may be a substrate or product of an enzyme in the metabolic pathway targeted by the drug. The metabolic pathway may be a nucleotide synthesis pathway, such as a pyrimidine synthesis pathway or a purine synthesis pathway. The metabolite may be an intermediate in a nucleotide synthesis pathway. For example, the metabolite may be N-carbamoylaspartate, dihydroorotate, orotate, orotidine 5′-monophosphate (OMP), or uridine monophoshpate (UMP).

The disorder may be any disorder, disease, or condition for which altering the activity of a metabolic pathway can be of therapeutic benefit. The disorder may be one in which inhibiting an enzyme in a metabolic pathway is of therapeutic benefit. The disorder may be cancer or an autoimmune disorder. The cancer may be leukemia, such as acute myeloid leukemia (AML), PTEN null prostate cancer, lung cancer, such as small cell lung cancer and non-small cell lung cancer, triple negative breast cancer (TNBC), glioma, multiple myeloma, acute lymphoblastic leukemia (ALL), neuroblastoma, or adult T cell leukemia/lymphoma (ATLL). The autoimmune disorder may be arthritis or multiple sclerosis.

The methods may include additional steps. For example, the method may include measuring the level of the metabolite in a sample obtained from the subject or providing the agent to the subject at the determined dose.

The sample may be a body fluid sample. For example, the body fluid may be plasma, blood, serum, urine, sweat, saliva, interstitial fluid, feces, or phlegm In an aspect, the invention provides methods for assessing the impact of a therapeutic agent on a tumor in real time. The methods include monitoring in real time a molecule that is associated with a metabolic pathway as the molecule moves through the metabolic pathway in a tumor in a subject and assessing the impact on the tumor of a therapeutic agent that has been administered to a subject based on results of the monitoring.

In another aspect, the invention provides methods for assessing the impact of a therapeutic agent on tumor in real time. The methods include monitoring in real time an oxygenation level in a tumor and assessing the impact on the tumor of a therapeutic agent that has been administered to a subject based on results of the monitoring step.

In another aspect, the invention provides methods for assessing the impact of a therapeutic agent on tumor in real time. The methods include monitoring in real time a molecule that is associated with a metabolic pathway as the molecule moves through the metabolic pathway in a tumor in a subject, monitoring in real time an oxygenation level in a tumor, and assessing the impact on the tumor of a therapeutic agent that has been administered to a subject based on results of the monitoring step.

The monitoring may include any suitable method. For example, monitoring the molecule in the tumor may include the use of hyperpolarization magnetic resonance imaging, and monitoring the oxygenation level of the tumor may include electron paramagnetic resonance (EPR) imaging.

The molecule may be a carbon molecule. The molecule may be or become associated with a metabolite in a metabolic pathway. For example, the metabolite may be N-carbamoylaspartate, dihydroorotate, orotate, orotidine 5′-monophosphate (OMP), or uridine monophoshpate (UMP).

The metabolic pathway may be any metabolic pathway, as described above. For example, the metabolic pathway may a nucleotide synthesis pathway.

The agent may be any therapeutic agent, as described above.

The methods may include quantifying the molecule. Quantifying the molecule may quantify the level of a metabolite in a metabolic pathway, such as dihydroorotate or orotate.

The methods may include determining, based on the levels of a metabolite, such as dihydroorotate or orotate, a dose of the therapeutic agent that is sufficient to inhibit an enzyme within the metabolic pathway, such as a nucleotide synthesis pathway, to an extent that at least one sign or symptom of the disorder is ameliorated, reduced, or eliminated.

The methods may include repeating one or more of the monitoring, assessing, and determining steps at different points in time. The methods may include adjusting the dose of the therapeutic agent based on results of the method from a subsequent point in time.

In another aspect, the invention provides devices for notifying a subject having a disorder that a dose of therapeutic agent that targets a metabolic pathway should be administered to the subject. The devices include a processor coupled to a memory unit that causes the processor to receive data that includes a dose of the therapeutic agent and the time the dose was received by the subject, generate a reminder that includes the time the next dose should be administered to the subject, and output the reminder to the subject. The time for administering the next dose to the subject is based on a relationship between the dose of the therapeutic agent and a threshold level of the metabolite, and administration of the next dose raises or maintains a level of the metabolite above the threshold. The threshold level is indicative that a sufficient amount of the agent is present in the subject to sufficiently alter the metabolic pathway to ameliorate, reduce, or eliminate at least one sign or symptom of the disorder.

The reminder may be any type of notification that can be perceived by a human. For example, the reminder may be an audible signal, a visual signal, a tactile signal, a vibration, or a combination thereof.

The reminder may be outputted to a component of the device. Additionally, or alternatively, the reminder may be outputted to a remote device.

Each of the time when the dose was received by the subject and the time when the next dose should be administered may include any temporal component. For example, each of the times may include a date, day of the week, hour, minute, second, or time zone.

The device may store information related to the time when the dose was received by the subject, the time when the next dose should be administered, or both. The information may be stored in the memory unit.

The process may perform calculations on the stored information. For example, the process may determine whether intervals between time points, such as times when individual doses are received by the subject, change over time. The processor may determine that the subject has developed resistance or is developing resistance to a therapeutic agent based on the stored information. For example, the processor may determine that the subject has developed resistance or is developing resistance to a therapeutic agent based on a change in the intervals over time, such as a decrease in the intervals over time, a change in the dose over time, such as an increase in the dose over time, or both.

The processor may output a recommendation for adjusting a therapeutic course for the subject. For example, the recommendation may include altering, e.g., increasing or decreasing, a dose, or altering, e.g., increasing or decreasing, an interval between doses. The recommendation may include administering a second therapeutic agent in addition to the first therapeutic agent. The recommendation may include a dose for administration of the second therapeutic agent, a time for administration of the second therapeutic agent, or both.

The processor may output stored information to a physician. For example, the processor may output information on doses of the therapeutic agent received by the subject, time points when the therapeutic agent was received by the subject, or both to a physician. The stored information may enable the physician to determine that the subject has developed or is developing resistance to the therapeutic agent. For example, the information may enable the physician to determine that the subject has developed resistance or is developing resistance to a therapeutic agent based on a change in the intervals of receiving the therapeutic agent over time, such as a decrease in the intervals over time, a change in the dose of the therapeutic agent over time, such as an increase in the dose over time, or both. The stored information may enable the physician to adjust the therapeutic course for the subject. For example, the stored information may enable the physician to alter the dose of the therapeutic agent, the time when the therapeutic agent should be administered, or both.

Other aspects of the invention relate specifically to Brequinar. Proliferating cancer cells show substantially different metabolic needs compared to normal differentiated cells as they require additional nutrients to support their high rates of proliferation. Success in targeting cancer cell metabolism will materialize from an improved understanding of exactly how cells control and consume nutrients into pathways that are essential for biosynthesis. As all cancer cells rely on this alteration in metabolism, these altered pathways represent strong therapeutic targets. However, discovering a therapeutic window between normal proliferating and cancer cells remains a major challenge as the metabolic requirements of these cells are similar. Thus, only a few molecules which target metabolic pathways have been established as a form of cancer treatment.

Brequinar is an example of a drug that can target metabolic pathways, particularly de novo biosynthesis of pyrimidine. However, this drug has failed in the past because it could not be delivered within an appropriate therapeutic window.

The invention recognizes that brequinar has failed in the past because it has not been dosed to achieve optimal enzyme inhibition. The invention solves that problem by using a highly sensitive marker of target engagement, a metabolite, to tailor a patient's dose to get an optimal Time Above Threshold (therapeutic window). Unlike prior approaches, the claimed invention is based on measuring target engagement instead of drug metabolism. In that manner, proper dosing of brequinar is achieved to kill cancer cells without causing harmful and toxic side effects to patients.

The de novo biosynthesis of pyrimidine is an essential metabolic pathway for nucleic acid synthesis. Although most cells meet their needs for nucleotides by reutilizing current ones through the salvage pathway, activated T cells and other rapidly proliferating cells, namely cancer cells are highly dependent on de novo nucleotide synthesis. Dihydroorotate dehydrogenase (DHODH) is the fourth sequential and rate-limiting enzyme in the de novo biosynthesis pathway of pyrimidines and it is the only enzyme found within the mitochondrial inner membrane of eukaryotes. Inhibition of this enzyme leads to intense reductions in cellular pyrimidine pools and eventually results in the failure of cells to proliferate.

Aspects of the invention are accomplished by measuring a trough dihydroorotate (DHO) level before a dose and using that level to dose adjust. In the historic studies with brequinar, there was high variability in the pharmacokinetic parameters. To overcome this, previous drug developers used plasma brequinar levels as a way to dose adjust but were not able to find an optimal dose and schedule for the drug. In some patients, brequinar is metabolized quickly, and there is not enough time above threshold of enzyme inhibition (and DHO), and hence too low a dose that is safe but will not produce any therapeutic effect. If brequinar is dosed at higher doses to achieve a therapeutic effect, the concentration of the drug results in too much time above threshold, causing toxic effects to be observed in healthy cells.

The invention recognizes that measuring the DHO level provides an accurate indication of target engagement of brequinar. Accurately knowing target engagement allows for appropriate doses of brequinar to be achieved that maintains the dosing within the therapeutic window.

With this understanding, the invention further recognizes that brequinar, and more generally, inhibitors of dihydroorotate dehydrogenase, can be used to treat certain cancers, such as acute myeloid leukemia (AML). AML afflicts over a million people worldwide. AML is incurable in the majority of cases and accounts for 1.8% of cancer deaths in the United States. Although recent decades have seen advances in our ability to diagnose and classify cases of AML, progress in treatment of AML has been less forthcoming: 90% of AML cases are treated with a therapeutic strategy that has remain unchanged for over 40 years.

The insights of the invention provide new compositions and methods for treating such cancers. Mainly, DHODH is present in all leukemic cells (essential enzyme). Differential metabolic sensitivity between leukemic cells and normal cells (i.e., “Metabolic Therapeutic Window”) presents a treatment opportunity. The compositions of the invention use inhibitors of dihydroorotate dehydrogenase (e.g., brequinar) on a novel dosing schedule to exploit the pro-differentiation effects and tolerability (lower dose with long exposure) between leukemic cells and normal cells. By linking the amount of DHODH inhibitor to the level of DHO, the compositions allow physicians to determine dosage of a drug based on engagement of the active pharmaceutical ingredient (API) with its target. Consequently, the compositions are optimized to achieve prolonged exposure to the API at a level sufficient to starve leukemic cells and to avoid the need for higher dosing that can harm other cells. The invention also provides methods of determining therapeutically effective doses of compositions that contain a DHODH inhibitor.

In addition to AML, the compositions and methods of the invention are more broadly useful for treating any diseases associated with unregulated or excessive DHODH activity, such as AML, arthritis, and multiple sclerosis. In particular, the compositions are useful for treating diseases that require sustained inhibition of DHODH. For example, recent studies have shown that the DHODH inhibitor brequinar decreases leukemia-initiating cell activity in mouse models of AML only when elevated levels of the compound are maintained in the plasma for extended periods.

The compositions and methods of the invention also enable physicians to tailor dosing regimens to individual patients. Because the rate of metabolism and elimination of a given drug varies among patients, the degree of target engagement by the API will differ among patients who have received the same drug and dosage. The level of DHO, however, is a universal indicator of DHODH inhibition across all patients. Thus, by monitoring levels of DHO in individual patients, the dose of a drug can be adjusted to achieve a desired level of DHODH inhibition on a case-by-case basis.

In another aspect, the invention provides compositions containing an inhibitor of DHODH in a therapeutically effective amount that raises or maintains a level of DHO above a threshold level in a subject for a period of more than 72 hours.

In another aspect, the invention provides compositions containing an inhibitor of DHODH in a therapeutically effective amount that results in a level of DHO being at least about 25 ng/mL in a subject.

In another aspect, the invention provides an oral formulation containing an inhibitor of DHODH in a therapeutically effective amount that raises or maintains a level of DHO above a threshold level in a subject for a period of more than 72 hours.

The threshold level of DHO may be measured in a sample obtained from a subject. The sample may be body fluid sample. For example, the body fluid may be plasma, blood, serum, urine, sweat, saliva, interstitial fluid, feces, or phlegm.

The threshold level of DHO may be a minimum level necessary for the DHODH inhibitor to provide a therapeutic benefit to a subject having a disorder. For example, the threshold level may be about 10 ng/mL, about 20 ng/mL, about 50 ng/mL, about 100 ng/mL, about 150 ng/mL, about 200 ng/mL, about 250 ng/mL, about 300 ng/mL, about 350 ng/mL, about 400 ng/mL, about 450 ng/mL, about 500 ng/mL, about 550 ng/mL, about 600 ng/mL, about 650 ng/mL, about 700 ng/mL, about 750 ng/mL, about 800 ng/mL, about 850 ng/mL, about 900 ng/mL, about 950 ng/mL, about 1000 ng/mL, about 1250 ng/ml, about 1500 ng/ml, about 1750 ng/ml, about 2000 ng/ml, about 2500 ng/ml, about 3000 ng/ml, about 3500 ng/ml, about 4000 ng/ml, about 4500 ng/ml, about 5000 ng/ml, about 6000 ng/ml, about 8000 ng/ml, about 10,000 ng/ml, about 12,000 ng/ml, about 15,000 ng/ml, about 20,000 ng/ml, about 25,000 ng/ml, about 30,000 ng/ml, about 40,000 ng/ml, about 50,000 ng/ml, about 75,000 ng/ml, about 100,000 ng/ml, about 150,000 ng/ml, about 200,000 ng/ml, about 300,000 ng/ml, or about 400,000 ng/ml.

The threshold level of DHO may be a maximum level above which a subject experiences one or more side effects of the DHODH inhibitor. For example, the threshold level may be about 100 ng/mL, about 150 ng/mL, about 200 ng/mL, about 250 ng/mL, about 300 ng/mL, about 350 ng/mL, about 400 ng/mL, about 450 ng/mL, about 500 ng/mL, about 550 ng/mL, about 600 ng/mL, about 650 ng/mL, about 700 ng/mL, about 750 ng/mL, about 800 ng/mL, about 850 ng/mL, about 900 ng/mL, about 950 ng/mL, about 1000 ng/mL, about 1250 ng/ml, about 1500 ng/ml, about 1750 ng/ml, about 2000 ng/ml, about 2500 ng/ml, about 3000 ng/ml, about 3500 ng/ml, about 4000 ng/ml, about 4500 ng/ml, about 5000 ng/ml, about 6000 ng/ml, about 8000 ng/ml, about 10,000 ng/ml, about 12,000 ng/ml, about 15,000 ng/ml, about 20,000 ng/ml, about 25,000 ng/ml, about 30,000 ng/ml, about 40,000 ng/ml, about 50,000 ng/ml, about 75,000 ng/ml, about 100,000 ng/ml, about 150,000 ng/ml, about 200,000 ng/ml, about 300,000 ng/ml, about 400,000 ng/ml, or about 500,000 ng/ml.

The threshold level of DHO may be a range of values. For example, the threshold level may from about 100 ng/mL to about 200 ng/mL, from about 150 ng/mL to about 200 ng/mL, from about 150 ng/mL to about 250 ng/mL, from about 200 ng/mL to about 250 ng/mL, or from about 200 ng/mL to about 300 ng/mL.

The DHODH inhibitor may be any agent that inhibits the activity of DHODH. The DHODH inhibitor may be a small molecule, protein, peptide, antibody, or polypeptide. The DHODH inhibitor may be brequinar, leflunomide, or teriflunomide. Brequinar may be in a modified form suitable for a therapeutic composition. For example, the DHODH inhibitor may be a brequinar analog, a brequinar derivative, a brequinar prodrug, a micellar formulation of brequinar, or a brequinar salt, such as a sodium salt.

The composition may contain the DHODH inhibitor at a defined amount. For example, the composition may contain brequinar sodium at about 400 mg/m², about 450 mg/m², about 500 mg/m², about 550 mg/m², about 600 mg/m², about 650 mg/m², about 700 mg/m², about 750 mg/m², or about 800 mg/m². The composition may contain another form of brequinar in amount equivalent to brequinar sodium at about 400 mg/m², about 450 mg/m², about 500 mg/m², about 550 mg/m², about 600 mg/m², about 650 mg/m², about 700 mg/m², about 750 mg/m², or about 800 mg/m².

The composition may be formulated for administration via a particular route. For example, the composition may be formulated for administration orally, intravenously, enterally, parenterally, dermally, buccally, topically, transdermally, by injection, subcutaneously, nasally, pulmonarily, or with or on an implantable medical device

The composition may contain a second therapeutic agent. The second therapeutic agent may inhibit a target other than DHODH. For example, the second agent may inhibit a glutaminase, the PI3K pathway, or orotidine 5′-monophosphate (OMP) decarboxylase.

The therapeutically effective amount of the DHODH inhibitor may be an amount sufficient to raise or maintain a level of DHO in a subject to ameliorate, reduce, or eliminate one or more signs or symptoms of a disorder in the subject. The therapeutically effective amount of the DHODH inhibitor may be an amount sufficient to raise or maintain a level of DHO in a subject above a threshold level, such as a threshold level described above. The therapeutically effective amount of the DHODH inhibitor may be an amount sufficient to raise or maintain a level of DHO in a subject for a period of time, such as 72 hours, 84 hours, 96 hours, 5 days, 6 days, 7 days, 10 days, 2 weeks, or more.

The therapeutically effective amount of the DHODH inhibitor may be an amount that does not result in the subject developing a side effect. For example, the therapeutically effective amount of the DHODH inhibitor may be an amount that does not result in the subject developing one or more of a blood disorder, nausea, vomiting, stomatitis, mucositis, skin rash, phlebitis, photosensitivity reactions, angioneurotic edema, and localized secondary hyperpigmentation of inflamed skin.

The composition may be provided as a single unit dosage. The composition may be provided as divided dosages.

In another aspect, the invention provides methods of determining a therapeutically effective dose of a DHODH inhibitor to be provided to a subject to treat a disorder. The therapeutically effective dose inhibits DHODH to an extent that at least one sign or symptom of the disorder is reduced or eliminated. The methods include determining a therapeutically effective dose of a DHODH inhibitor based on a measured level of DHO in a sample from a subject.

The therapeutically effective dose of the DHODH inhibitor may be a dose that raises or maintains a level of DHO above a threshold level in a sample obtained from the subject for a period of more than 72 hours. The threshold level may be any threshold level, such as those described above. The sample may be any sample, such as those described above.

In another aspect, the invention provides methods of adjusting a dosing regimen of a DHODH inhibitor to treat a disorder in a subject that is currently on the dosing regimen. The methods include receiving information regarding a measured level of dihydroorotate (DHO) in a sample from a subject, comparing the received information to a reference that provides an association of a measured level of DHO with a recommended dosage adjustment of a DHODH inhibitor, and adjusting the dosing regimen of the DHODH inhibitor so that a next dose of the DHODH inhibitor in the dosing regimen results in a level of DHO being raised or maintained above a threshold level indicative that the amount of the DHODH inhibitor in the subject is sufficient to reduce or eliminate at least one sign or symptom of the disorder.

In the methods of determining a therapeutically effective dose of a DHODH inhibitor or adjusting a dosing regimen of a DHODH inhibitor, the DHODH inhibitor may be any DHODH inhibitor, such as those described above.

The disorder may be any disease, disorder, or condition for which a DHODH inhibitor would provide a therapeutic benefit. For example, the disorder may be cancer, such as leukemia (e.g., acute myeloid leukemia) or prostate cancer, or an autoimmune disease, such as multiple sclerosis or arthritis (e.g., rheumatoid arthritis or psoriatic arthritis).

The methods may include determining a time point when the therapeutically effective dose of the DHODH inhibitor should be provided to the subject. The methods may include providing the DHODH inhibitor to the subject at the therapeutically effective dose.

The recommended dosage adjustment may be an increase the dosage, decrease in the dosage, or no change in the dosage. The recommendation may include a value by which the dosage should be increased or decreased.

The information regarding a measured level of DHO in a sample from a subject may include a measured level from one sample obtained from the subject or measured levels from multiple samples obtained from the subject. The information may include a time point indicating when each sample was obtained from the subject.

The dosing regimen may be adjusted in any manner. For example, the dosing regimen may be adjusted by adjusting the dose, the time for delivering the dose, or both. The adjustment may include determining a time point for delivering the dose.

The methods may include providing the DHODH inhibitor to the subject at the determined dose. The DHODH inhibitor may be provided orally, intravenously, enterally, parenterally, dermally, buccally, topically, transdermally, by injection, subcutaneously, nasally, pulmonarily, or with or on an implantable medical device. The DHODH inhibitor may be provided as a single unit dosage, or it may be provided as divided dosages.

In another aspect, the invention provides methods of making a 2-(2′-halo-1-1′-biphenyl-4-yl)-quinoline carboxylic acid. The methods include incubating a compound of formula (I) with a compound of formula (II) in a mixture containing a base and adding an acid to the mixture, thereby creating a compound of formula (III) according to following reaction:

in which:

R₁, R₂, R₃, and R₄ are independently H, F, Cl, Br, I, CH₃, CF₃, SCH₃ or CH₂ CH₃, at least two of R₁, R², R₃, and R₄ being H;

R₅ is H, alkoxy of 1-3 carbon atoms, or alkyl of 1-2 carbon atoms;

R₆ and R₇ are independently H, F, Cl, Br, alkyl of 1-5 carbon atoms, NO₂, OH, CF₃ or OCH₃;

X is a halogen; and

the incubating step includes at least one of:

-   -   incubating the mixture at a temperature of from about 60° C. to         about 70° C.,     -   the mixture containing a molar ratio of the base to the compound         of formula (II) of from about 5:1 to about 8:1, and     -   incubating the mixture for from about 15 hours to about 30         hours.

The incubating step may include one or more of incubating the mixture at a temperature of from about 60° C. to about 70° C., using a mixture containing a molar ratio of the base to the compound of formula (II) of from about 5:1 to about 8:1, and incubating the mixture for from about 15 hours to about 30 hours.

The method may include a minimum yield of the compound of formula (III). For example, the yield of the compound of formula (III) may be at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%.

The base may be any suitable base. For example, the base may be KOH, NaOH, or NH₄OH.

The alcohol may be any suitable alcohol. For example, the alcohol may be methanol, ethanol, 1-propanol, 2-propanol, butanol, 2-methyl-1-propanol, or pentanol.

The acid may be any suitable acid. For example, the acid may be HCl or acetic acid.

The compound of formula (III) may be brequinar. The compound of formula (III) may have the structure represented by formula (IV):

The invention also recognizes that each year about 25,000 people in the United States are newly diagnosed with some form of brain cancer. The five-year survival is about 35% for all patients with malignant brain tumors and about 5% for patients with glioblastoma multiforme, the most common type of primary brain tumor. Brain cancer is costly in financial terms as well. A 2011 study found that the average estimated lifetime economic cost of a case of brain cancer is 1.9 million Australian dollars, the highest of any type of cancer.

Current methods for treating brain cancer are plagued by risks and side effects. Treatment typically includes surgery, radiation therapy, chemotherapy, or some combination of these three approaches. Surgery achieves the best outcomes, but many brain tumors are intractable to surgery due to their anatomical location. Moreover, craniotomy, the most common surgical approach to treat brain cancer, carries a high risk of infection, and patients experience significant pain during recovery. Radiotherapy to the brain is relatively painless for the patient but can cause swelling of the brain, which produces its own set of symptoms that may require treatment, and long-term cognitive decline. Chemotherapy is ineffective for treating most brain cancers because many chemotherapeutic drugs do not traverse the blood-brain barrier. Although one anti-cancer drug that does cross the blood-brain barrier, temozolomide, has been shown to delay progression of glioblastoma multiforme, tumors that recur in temozolomide-treated patients have a higher mutational burden and are more aggressive. Thus, the predominant existing therapies for treating brain cancer all have severe limitations, and the disease continues to take its toll in both human lives and financial resources.

The invention provides methods of treating brain cancer, such as gliomas of neuroepithelial tissue and neuroblastoma, by providing an inhibitor of an enzyme in a metabolic pathway. Due to their rapid growth rate, cancer cells are more dependent on certain metabolic pathways, such as those involved in nucleotide synthesis, than are normal cells. Therefore, by providing an agent that reduces the activity of such pathways, cancer cells can be selectively killed. The invention recognizes that enzyme inhibitors that pass through blood-brain barrier represent a potent new class of anti-cancer agents for treatment of brain cancer.

An exemplary method of the invention entails treating brain cancer using an inhibitor of dihydroorotate dehydrogenase (DHODH), and enzyme involved in synthesis of uridine monophosphate (UMP). For certain cancers, DHODH inhibitors, such as brequinar, kill cancer cells and have minimal adverse effect on healthy tissue when provided at appropriate dosages. The invention further recognizes that engagement of a DHODH inhibitor with the enzyme can be monitored by analysis of levels of DHO, a substrate of DHODH, in samples obtained from the patient. Therefore, methods of the invention enable physicians to ensure that a DHODH inhibitor is administered in a therapeutically effective amount to treat brain cancer.

Methods of the invention provide therapeutic strategies for treating brain cancer that overcome many of the limitations of prior methods. Significantly, the methods avoid the high risk of infection associated with surgery. In addition, in contrast to surgery and radiotherapy, the methods are not constrained by the number and anatomical location of tumors. Compared to prior chemotherapeutic approaches, the methods of the invention are more broadly applicable and thus can be used to treat a variety of types of brain cancer.

In another aspect, the invention provides methods of treating brain cancer in a subject by providing to the subject an agent that crosses the blood-brain barrier and that inhibits a metabolic pathway in a cancerous cell in the brain of the subject.

Any metabolic pathway may be targeted, provided that cancer cells are more sensitive to activity of the pathway than are normal cells. For example, the metabolic pathway may be nucleotide synthesis pathway, such as a pyrimidine synthesis pathway or a purine synthesis pathway. The metabolic pathway may be a pathway for the synthesis of UMP.

The enzyme may be any enzyme in the metabolic pathway. For example, the enzyme may be DHODH or orotidine 5′-monophosphate (OMP) decarboxylase.

The agent may be any agent that inhibits an enzyme in the metabolic pathway. The agent may be a small molecule, protein, peptide, antibody, or polypeptide. The agent may be brequinar, leflunomide, or teriflunomide. Brequinar may be in a modified form suitable for a therapeutic composition. For example, the agent may be a brequinar analog, a brequinar derivative, a brequinar pro-drug, a micellar formulation of brequinar, or a brequinar salt, such as a sodium salt.

The brain cancer may be any cancer of the brain or central nervous system. The brain cancer may include a tumor of neuroepithelial tissue, cranial or paraspinal nerves, the meninges, the hematopoietic system, germ cells, or the sellar region. The brain cancer may include cancer cells derived from neuroepithelial cells, meningeal cells, or hematopoietic cells. The brain cancer may be astrocytoma, glioma, meningioma, or neuroblastoma.

The methods may include receiving a measured level of a metabolite in the metabolic pathway in a sample from the subject. The measured level of the metabolite may be received prior to, during, or subsequent to providing the agent. The measured level of the metabolite may be compared to a threshold level, and measured levels below the threshold level may indicate that one or more additional doses of the agent are required.

The methods may include using the measured level of the metabolite to determine a dose of the agent required to raise or maintain the measured level of the metabolite above the threshold level. The methods may include providing the agent in the determined dose.

The metabolite may be a substrate or product of the enzyme that is inhibited by the agent. For example, the metabolite may be dihydroorotate or orotate.

The sample may be body fluid sample. For example, the body fluid may be plasma, blood, serum, urine, sweat, saliva, interstitial fluid, feces, or phlegm.

In another aspect, the invention provides methods of treating brain cancer in a subject by providing a DHODH inhibitor to the subject. Preferably, the DHODH inhibitor is an agent that crosses the blood-brain barrier.

The DHODH inhibitor may be a small molecule, protein, peptide, antibody, or polypeptide. The DHODH inhibitor may be brequinar, leflunomide, or teriflunomide. Brequinar may be in a modified form suitable for a therapeutic composition. For example, the DHODH inhibitor may be a brequinar analog, a brequinar derivative, a brequinar pro-drug, a micellar formulation of brequinar, or a brequinar salt, such as a sodium salt.

The brain cancer may be any cancer of the brain or central nervous system, such as those described above.

The methods may include receiving a measured level of a metabolite in the metabolic pathway in a sample from the subject. The measured level of the metabolite may be received prior to, during, or subsequent to providing the DHODH inhibitor. The measured level of the metabolite may be compared to a threshold level, and measured levels below the threshold level may indicate that one or more additional doses of the DHODH inhibitor are required.

The sample may be any sample obtained from a subject, such as those described above. For example, the sample may be a plasma sample.

The methods may include using the measured level of the metabolite to determine a dose of the DHODH inhibitor required to raise or maintain the measured level of the metabolite above the threshold level. The methods may include providing the agent in the determined dose.

The metabolite may be a metabolite is in a nucleotide synthesis pathway. For example, the metabolite may be dihydroorotate or orotate.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-FIG. 1C are a series of graphs showing levels of brequinar and DHO in three patients that have received a single dose of brequinar according to the same dosing regimen.

FIG. 2A-FIG. 2L are a series of graphs showing levels of brequinar and DHO in three patients that have received multiple doses of brequinar according to the same dosing regimen.

FIG. 3 is a flow chart illustrating an example of determining dose of a DHODH inhibitor for a patient according to an embodiment of the invention.

FIG. 4 is a scatter plot illustrating the concentration of brequinar in subject plasma over time when administered twice weekly.

FIG. 5 is a scatter plot illustrating the bioavailability of an IV formulation of brequinar as compared to an oral dosage form.

FIG. 6 is a scatter plot illustrating the concentration of brequinar in mice at a dose of 50 mg/kg over time.

FIG. 7 is a scatter plot illustrating the baseline DHO levels in random cancer patients and healthy patients, as reported in Table 5.

FIG. 8 is a scatter plot illustrating the concentrations of pyrazofurin and orotate in murine plasma over time when pyrazofurin is administered as a single dose (20 mg/kg).

FIG. 9 is a scatter plot illustrating the concentrations of pyrazofurin and orotate in murine plasma over time when pyrazofurin is administered as a single dose (20 mg/kg) on a log scale.

FIG. 10 is a graph showing the therapeutic benefit of a drug that targets a metabolic pathway as a function of levels of a metabolite that is an intermediate in the pathway.

FIG. 11 is a schematic showing the role of DHODH in pyrimidine synthesis.

FIG. 12 is graph of the percentage maximum effect of brequinar toward SARS-CoV-2 as a function of brequinar concentration.

FIG. 13 is a graph of the IC₅₀ of remdesivir toward SARS-CoV-2 as a function of brequinar concentration.

FIG. 14 is a graph of brequinar concentration in the plasma of a patient during a 5-day course of once-per-day doses.

FIG. 15 is graph of tumor size in mice treated with brequinar alone, ribavirin alone, or brequinar and ribavirin in combination.

FIG. 16 is graph of tumor size in mice treated with 50 mg/kg brequinar and 100 mg/kg ribavirin.

FIG. 17 is graph of tumor size in mice treated with 50 mg/kg brequinar and 50 mg/kg ribavirin.

FIG. 18 is a graph of percentage maximal effect of brequinar as a function of brequinar concentration.

FIG. 19 is graph showing the effect of brequinar on the anti-SARS-CoV-2 efficacy of remdesivir.

FIG. 20 is a graph showing the levels of brequinar in the plasma of a subject that receives a single daily dose of brequinar for five consecutive days.

FIG. 21 is a graph showing both the levels of intracellular pyrimidines and the levels of brequinar in the plasma of a subject that receives a single daily dose of brequinar for five consecutive days.

FIG. 22 is a graph showing both the levels of viral replication and the levels of brequinar in the plasma of a subject that receives a single daily dose of brequinar for five consecutive days.

DETAILED DESCRIPTION

The invention provides methods of treating viral infections, such as COVID-19, using inhibitors of nucleotide synthesis pathways. In some embodiments, the methods include agents, such as brequinar, that interfere with synthesis of pyrimidine-based nucleotides by inhibiting dihydroorotate dehydrogenase (DHODH). Viruses need a steady supply of nucleotides to reproduce within cells, and nucleotide starvation blocks viral replication. The methods may include other classes of drugs, such as inhibitors of purine synthesis or other antiviral drugs, in combination with pyrimidine synthesis inhibitors.

The invention also provides methods of treating viral respiratory infections by providing brequinar according to a dosing regimen that delivers the drug to the lungs at sustained, elevated levels that prevent viral replication. In such methods, dosing regimens maintain brequinar levels in the lungs at concentrations sufficient to inhibit pyrimidine synthesis and trigger nucleotide starvation. The dosing regimens may be calibrated based to administer a defined amount of brequinar to the subject or to attain a defined concentration of the drug in the lungs. The dosing regimens may include dosage-free periods that allow nucleotide pools to be replenished to support cellular homeostasis. Because brequinar readily enters the lungs from the blood, the drug may be provided by any suitable route of administration, such as intravenously, topically, or orally, in methods of the invention. The methods may include combination therapies in which a brequinar dosing regimen is paired with administration of another agent, such as an antiviral agent.

Metabolites

The invention provides methods that allow real-time determination of therapeutically effective dosing regimens of drugs that include an enzyme inhibitor as an active pharmaceutical ingredient (API). The methods are based on the insight that the extent to which the target enzyme is engaged by the inhibitor can be evaluated based on measured levels of a metabolite in a pathway in which the enzyme functions. In particular, target engagement can be assessed from levels of a substrate of the enzyme. From the measured level of a metabolite in a sample obtained from a patient, the methods allow a physician to determine an appropriate amount of drug that contains an enzyme inhibitor to administer to the patient to alleviate a sign or symptom of a disorder and minimize undesirable side effects of the drug.

The methods of the invention greatly improve the utility of drugs that have large interpatient variability in drug metabolism or a narrow therapeutic window, i.e., drugs for which the range between doses necessary to achieve therapeutic effect and doses that cause toxicity is small. Administration of such drugs requires precise dosing and typically includes monitoring of their effects on patients. Monitoring often involves measurement of the level of the API or a metabolic product of the API in the patient's body. However, patients vary widely in their ability to metabolize drugs and in how drugs affect targets in their bodies, so analysis of the API or a metabolic product thereof provides an incomplete readout of the efficacy of a given drug in an individual patient. The invention overcomes this limitation by using levels of a metabolite in an enzymatic pathway as a metric of engagement of the API with its target enzyme. Whereas patient variability makes drug efficacy difficult to ascertain precisely from levels of an API or a metabolic product of the API, levels of a metabolite in the pathway of the API's target are universal indicators of target engagement. Thus, because the dosing regimen is determined based on levels of the metabolite rather than levels of the drug, the methods of the invention afford greater precision in the dosage and timing of drug administration. Consequently, the methods enable the safe and effective treatment of a variety of conditions using therapeutic agents that are ineffective or too dangerous under prior methods.

According to methods of the invention, drug dosage is determined based on real-time measured levels of a metabolite in a patient. The levels may be measured in a sample, such as plasma sample, obtained from a patient. In such embodiments, the methods permit rapid, convenient monitoring of patients. Alternatively, levels of the metabolite may be measured in a tumor in vivo. Thus, the invention also provides methods that allow direct, real-time assessment of the effect of a therapeutic agent on a tumor in the patient's body.

The invention further provides devices, such as wearable electronic devices, that provide reminders to a patient regarding drug dosing, such as the dosage of a drug or time for administration. The notifications that the devices provide are based on one or more measured values of a metabolite in a sample obtained from the patient. Thus, the devices incorporate the aforementioned advantages of the methods provided herein.

Metabolites as Indicators of Target Engagement

Methods of the invention include determining the dosage of a drug based on a measured level of a metabolite in a sample obtained from a subject. The metabolite may be any molecule that provides an indication of target engagement by the API of the drug. In embodiments of the invention, the API is an inhibitor of an enzyme in a metabolic pathway, and the metabolite is an intermediate the pathway. Preferably, the metabolite the API is an inhibitor of an enzyme in a metabolic pathway, and the metabolite is a substrate of the enzyme.

Nucleotide synthesis pathways are of particular therapeutic interest. The high proliferation rate of cancer cells often places increased demand on nucleotide synthesis pathways. Consequently, enzymes that function in such pathways are useful targets for antineoplastic drugs. Specifically, drugs that inhibit enzymes require for nucleotide synthesis have been investigated for treating cancer. Therefore, levels of metabolites in nucleotide synthesis pathways are useful for evaluating the extent to which the APIs in such drugs are engaging their targets in vivo.

Pyrimidine biosynthesis involves a sequence of step enzymatic reactions that result in the conversion of glutamine to uridine monophosphate as shown below:

Several of the enzymes in the pyridine synthesis pathway are targets of drugs or drug candidates. For example, inhibitors of the following enzymes have been investigated as therapeutic agents: aspartate carbamoyltransferase (also known as aspartate transcarbamoylase or ATCase), which catalyzes the conversion of carbamoyl phosphate to carbamoyl aspartate; dihydroorotate dehydrogenase (DHODH), which catalyzes conversion of dihydroorotate (DHO) to orotate; and OMP decarboxylase (OMPD), which catalyzes conversion of orotidine monophosphate (OMP) to uridine monophosphate (UMP).

One element of the invention is recognition of the utility of DHO as an indicator of target engagement by DHODH inhibitors. One advantage of DHO is that cell membranes are permeable to the molecule. DHODH is localized to the mitochondrial inner membrane within cells, making direct measurement of enzyme activity difficult. However, DHO, which accumulates when DHODH is inhibited, diffuses out of cells and into the blood, which can be easily sampled. Another insight of the invention is that DHO is sufficiently stable that levels of the metabolite can be measured reliably. Previously, DHO was considered too unstable at ambient temperatures to be quantified accurately and was thus deemed unsuitable as an indicator of DHODH inhibition. However, the methods provided herein permit detection of DHO in plasma samples. Thus, by analyzing levels of DHO in blood or blood products, one can readily assess target engagement of a DHODH inhibitor.

In an analogous manner, orotate and OMP can serve as indicators for target engagement of OMP decarboxylase inhibitors. For example, inhibition of OMP decarboxylase leads to increased plasma levels of orotate, so measurement of plasma orotate levels is useful for assessing the effect of agents that target OMP decarboxylase.

The methods of the invention are applicable for therapeutic agents that regulate the activity of other metabolic pathways as well. Examples of such pathways include the purine synthesis pathway, which is targeted by methotrexate and 6-mercaptopurine and in which an enzyme inosine-5′-monophosphate dehydrogenase (IMPDH) may be targeted; the anandamide degradation pathway, including the enzyme fatty acid amide hydrolase, which is targeted by a variety of inhibitors and activators; and glycolysis, the citric acid cycle, and the balance between the two, which are targeted by various drug candidates; the pentose phosphate pathway; and the beta-oxidation pathway.

Measuring the Level of a Metabolite in a Sample

Methods of the invention include analysis of a measured level of metabolite in a sample. The methods may include measurement of the metabolite.

In some embodiments, the metabolite is measured by mass spectrometry, optionally in combination with liquid chromatography. Molecules may be ionized for mass spectrometry by any method known in the art, such as ambient ionization, chemical ionization (CI), desorption electrospray ionization (DESI), electron impact (EI), electrospray ionization (ESI), fast-atom bombardment (FAB), field ionization, laser ionization (LIMS), matrix-assisted laser desorption ionization (MALDI), paper spray ionization, plasma and glow discharge, plasma-desorption ionization (PD), resonance ionization (RIMS), secondary ionization (SIMS), spark source, or thermal ionization (TIMS). Methods of mass spectrometry are known in the art and described in, for example, U.S. Pat. Nos. 8,895,918; 9,546,979; 9,761,426; Hoffman and Stroobant, Mass Spectrometry: Principles and Applications (2nd ed.). John Wiley and Sons (2001), ISBN 0-471-48566-7; Dass, Principles and practice of biological mass spectrometry, New York: John Wiley (2001) ISBN 0-471-33053-1; and Lee, ed., Mass Spectrometry Handbook, John Wiley and Sons, (2012) ISBN: 978-0-470-53673-5, the contents of each of which are incorporated herein by reference.

In certain embodiments, a sample can be directly ionized without the need for use of a separation system. In other embodiments, mass spectrometry is performed in conjunction with a method for resolving and identifying ionic species. Suitable methods include chromatography, capillary electrophoresis-mass spectrometry, and ion mobility. Chromatographic methods include gas chromatography, liquid chromatography (LC), high-pressure liquid chromatography (HPLC), hydrophilic interaction chromatography (HILIC), ultra-performance liquid chromatography (UPLC), and reversed-phase liquid chromatography (RPLC). In a preferred embodiment, liquid chromatography-mass spectrometry (LC-MS) is used. Methods of coupling chromatography and mass spectrometry are known in the art and described in, for example, Holcapek and Brydwell, eds. Handbook of Advanced Chromatography/Mass Spectrometry Techniques, Academic Press and AOCS Press (2017), ISBN 9780128117323; Pitt, Principles and Applications of Liquid Chromatography-Mass Spectrometry in Clinical Biochemistry, The Clinical Biochemist Reviews. 30(1): 19-34 (2017) ISSN 0159-8090; Niessen, Liquid Chromatography-Mass Spectrometry, Third Edition. Boca Raton: CRC Taylor & Francis. pp. 50-90. (2006) ISBN 9780824740825; Ohnesorge et al., Quantitation in capillary electrophoresis-mass spectrometry, Electrophoresis. 26 (21): 3973-87 (2005) doi:10.1002/elps.200500398; Kolch et al., Capillary electrophoresis-mass spectrometry as a powerful tool in clinical diagnosis and biomarker discovery, Mass Spectrom Rev. 24 (6): 959-77. (2005) doi:10.1002/mas.20051; Kanu et al., Ion mobility-mass spectrometry, Journal of Mass Spectrometry, 43 (1): 1-22 (2008) doi:10.1002/jms.1383, the contents of which are incorporated herein by reference.

A sample may be obtained from any organ or tissue in the individual to be tested, provided that the sample is obtained in a liquid form or can be pre-treated to take a liquid form. For example and without limitation, the sample may be a blood sample, a urine sample, a serum sample, a semen sample, a sputum sample, a lymphatic fluid sample, a cerebrospinal fluid sample, a plasma sample, a pus sample, an amniotic fluid sample, a bodily fluid sample, a stool sample, a biopsy sample, a needle aspiration biopsy sample, a swab sample, a mouthwash sample, a cancer sample, a tumor sample, a tissue sample, a cell sample, a synovial fluid sample, a phlegm sample, a saliva sample, a sweat sample, or a combination of such samples. The sample may also be a solid or semi-solid sample, such as a tissue sample, feces sample, or stool sample, that has been treated to take a liquid form by, for example, homogenization, sonication, pipette trituration, cell lysis etc. For the methods described herein, it is preferred that a sample is from plasma, serum, whole blood, or sputum.

The sample may be kept in a temperature-controlled environment to preserve the stability of the metabolite. For example, DHO is more stable at lower temperatures, and the increased stability facilitates analysis of this metabolite from samples. Thus, samples may be stored at 4° C., −20° C., or −80° C.

In some embodiments, a sample is treated to remove cells or other biological particulates. Methods for removing cells from a blood or other sample are well known in the art and may include e.g., centrifugation, sedimentation, ultrafiltration, immune selection, etc.

The subject may be an animal (such as a mammal, such as a human). The subject may be a pediatric, a newborn, a neonate, an infant, a child, an adolescent, a pre-teen, a teenager, an adult, or an elderly patient. The subject may be in critical care, intensive care, neonatal intensive care, pediatric intensive care, coronary care, cardiothoracic care, surgical intensive care, medical intensive care, long-term intensive care, an operating room, an ambulance, a field hospital, or an out-of-hospital field setting.

The sample may be obtained from an individual before or after administration to the subject of an agent that alters activity of a metabolic pathway, such as inhibitor of an enzyme in the pathway. For example, the sample may be obtained 1 hour, 2 hours, 4 hours, 6 hours, 8 hours, 12 hours, 24 hours, 36 hours, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days or more before administration of an agent, or it may be obtained 1 hour, 2 hours, 4 hours, 6 hours, 8 hours, 12 hours, 24 hours, 36 hours, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days or more after administration of an agent.

Determining Dosing Regimens

Methods of the invention include determining a dosing regimen of an agent that alters a metabolic pathway, such as an inhibitor of an enzyme in the pathway, for a subject. The dosing regimen may include a dose, i.e., an amount, of the agent that should be administered. The dosing regimen may include a time point for administration of a dose of the agent to the subject. Because the dosing regimen is based on one or more measured levels of a metabolite in a sample obtained from the subject, the dosing regimen is tailored to an individual subject, e.g., a patient. Consequently, the methods of the invention provide customized dosing regimens that account for variability in pharmacokinetic properties, i.e., metabolism of the API by the subject, and pharmacodynamics properties, effect of the API on its target, among individuals.

The dosing regimen may be determined by comparing a measured level of a metabolite in a sample obtained from a subject to a reference that provides an association between the measured level and a recommended dosage adjustment of the agent. For example, the reference may provide a relationship between administration of the agent and levels of the metabolite in the subject. The relationship can be empirically determined from a known dose and time of administration of the agent and measured levels of the metabolite at one or more subsequent time points. The reference may include a relationship between measured levels of the agent or a metabolic product of the agent and measured levels of the metabolite.

From the comparison between the measured level of the metabolite and the reference, a dosing regimen may then be determined. The dosing regimen may include a dosage of the agent, a time for administration of the dosage, or both. The dosing regimen may be determined de novo, or it may comprise an adjustment to a previous dosing regimen, such as an adjustment in the dosage, the interval between administration of dosages, or both.

The dosing regimen is designed to deliver the agent to the subject in an amount that achieves a therapeutic effect. The therapeutic effect may be a sign or symptom of a disease, disorder, or condition. The therapeutic effect may be inhibition of an enzyme in the metabolic pathway, or it may be a change in an indicator of inhibition of an enzyme in a metabolic pathway. The indicator may be a metabolite in the pathway, and the therapeutic effect may be an increase or decrease in levels of the metabolite. The therapeutic effect may be a decrease in number of cancer cells, a decrease in proliferation of cancer cells, an increase in differentiation of pre-cancerous cells, such as myeloblasts, complete remission of cancer, complete remission with incomplete hematologic recovery, morphologic leukemia-free stat, or partial remission. Increased differentiation of myeloblasts may be assessed by one or more of expression of CD14, expression of CD11b, nuclear morphology, and cytoplasmic granules.

The dosing regimen may ensure that levels of a metabolite are raised or maintained a minimum threshold required to achieve a certain effect. For example, the dosing regimen may raise or maintain levels of the metabolite above a threshold level in the subject for a certain time period. The time period may include a minimum, a maximum, or both. For example, the dosing regimen may raise or maintain levels of the metabolite above the threshold level for at least 6 hours, 12, hours, 24 hours, at least 48 hours, at least 60 hours, at least 72 hours, at least 84 hours, at least 96 hours, at least 5 days, at least 6 days, at least 7 days, at least 10 days, at least 2 weeks, or more. The dosing regimen may raise or maintain levels of the metabolite above the threshold level for not more than 24 hours, not more than 36 hours, not more than 48 hours, not more than 60 hours, not more than 72 hours, not more than 84 hours, not more than 96 hours, not more than 5 days, not more than 6 days, not more than 7 days, not more than 10 days, or not more than 2 weeks. The dosing regimen may raise or maintain levels of the metabolite above the threshold level for at least 72 hours but not more than 96 hours, for at least 72 hours but not more than 5 days, for at least 72 hours but not more than 6 days, for at least 72 hours but not more than 7 days, for at least 96 hours but not more than 7 days.

The dosing regimen may ensure that levels of a metabolite do not exceed or are maintained below a maximum threshold that is associated with toxicity. Levels of the metabolite above a maximum threshold may indicate that the agent is causing or is likely to cause an adverse event in the subject. For example and without limitation, adverse events include abdominal pain, anemia, anorexia, blood disorders, constipation, diarrhea, dyspepsia, fatigue, fever, granulocytopenia, headache, infection, leukopenia, mucositis, nausea, pain at the injection site, phlebitis, photosensitivity, rash, somnolence, stomatitis, thrombocytopenia, and vomiting.

The dosing regimen may include a time point for administration of one or more subsequent doses to raise or maintain levels of the metabolite above a threshold level for a certain time period. The time point for administration of a subsequent dose may be relative to an earlier time point. For example, the time point for administration of a subsequent dose may be relative to a time point when a previous dose was administered or a time point when a sample was obtained from a subject.

The dosing regimen may include a schedule for administration of doses. For example, doses may be administered at regular intervals, such as every 24 hours, every 36 hours, every 48 hours, every 60 hours, every 72 hours, every 84 hours, every 96 hours, every 5 days, every 6 days, every week, every 2 weeks, every 3 weeks, or every 4 weeks. Alternatively, doses may be administered according to a schedule that does not require precisely regular intervals. For example, doses may be administered once per week, twice per week, three times per week, four times per week, once per month, twice per month, three times per month, four times per month, five times per month, or six times per month.

For example and without limitation, a dosing regimen for administration of a therapeutic agent, such brequinar, e.g., brequinar sodium, to a human subject may be as follows: 100 mg/m², administered intravenously twice weekly; 125 mg/m², administered intravenously twice weekly; 150 mg/m², administered intravenously twice weekly; 200 mg/m², administered intravenously twice weekly; 250 mg/m², administered intravenously twice weekly; 275 mg/m², administered intravenously twice weekly; 300 mg/m², administered intravenously twice weekly; 350 mg/m², administered intravenously twice weekly; 400 mg/m², administered intravenously twice weekly; 425 mg/m², administered intravenously twice weekly; 450 mg/m², administered intravenously twice weekly; 500 mg/m², administered intravenously twice weekly; 550 mg/m², administered intravenously twice weekly; 600 mg/m², administered intravenously twice weekly; 650 mg/m², administered intravenously twice weekly; 700 mg/m², administered intravenously twice weekly; 750 mg/m², administered intravenously twice weekly; 800 mg/m², administered intravenously twice weekly; 100 mg/m², administered intravenously every 72 hours; 125 mg/m², administered intravenously every 72 hours; 150 mg/m², administered intravenously every 72 hours; 200 mg/m², administered intravenously every 72 hours; 250 mg/m², administered intravenously every 72 hours; 275 mg/m², administered intravenously every 72 hours; 300 mg/m², administered intravenously every 72 hours; 350 mg/m², administered intravenously every 72 hours; 400 mg/m², administered intravenously every 72 hours; 425 mg/m², administered intravenously every 72 hours; 450 mg/m², administered intravenously every 72 hours; 500 mg/m², administered intravenously every 72 hours; 550 mg/m², administered intravenously every 72 hours; 600 mg/m², administered intravenously every 72 hours; 650 mg/m², administered intravenously every 72 hours; 700 mg/m², administered intravenously every 72 hours; 750 mg/m², administered intravenously every 72 hours; 800 mg/m², administered intravenously every 72 hours; 100 mg/m², administered intravenously every 84 hours; 125 mg/m², administered intravenously every 84 hours; 150 mg/m², administered intravenously every 84 hours; 200 mg/m², administered intravenously every 84 hours; 250 mg/m², administered intravenously every 84 hours; 275 mg/m², administered intravenously every 84 hours; 300 mg/m², administered intravenously every 84 hours; 350 mg/m², administered intravenously every 84 hours; 400 mg/m², administered intravenously every 84 hours; 425 mg/m², administered intravenously every 84 hours; 450 mg/m², administered intravenously every 84 hours; 500 mg/m², administered intravenously every 84 hours; 550 mg/m², administered intravenously every 84 hours; 600 mg/m², administered intravenously every 84 hours; 650 mg/m², administered intravenously every 84 hours; 700 mg/m², administered intravenously every 84 hours; 750 mg/m², administered intravenously every 84 hours; 800 mg/m², administered intravenously every 84 hours; 100 mg/m², administered intravenously every 96 hours; 125 mg/m², administered intravenously every 96 hours; 150 mg/m², administered intravenously every 96 hours; 200 mg/m², administered intravenously every 96 hours; 250 mg/m², administered intravenously every 96 hours; 275 mg/m², administered intravenously every 96 hours; 300 mg/m², administered intravenously every 96 hours; 350 mg/m², administered intravenously every 96 hours; 400 mg/m², administered intravenously every 96 hours; 425 mg/m², administered intravenously every 96 hours; 450 mg/m², administered intravenously every 96 hours; 500 mg/m², administered intravenously every 96 hours; 550 mg/m², administered intravenously every 96 hours; 600 mg/m², administered intravenously every 96 hours; 650 mg/m², administered intravenously every 96 hours; 700 mg/m², administered intravenously every 96 hours; 750 mg/m², administered intravenously every 96 hours; 800 mg/m², administered intravenously every 96 hours; 100 mg/m², administered orally twice weekly; 125 mg/m², administered orally twice weekly; 150 mg/m², administered orally twice weekly; 200 mg/m², administered orally twice weekly; 250 mg/m², administered orally twice weekly; 275 mg/m², administered orally twice weekly; 300 mg/m², administered orally twice weekly; 350 mg/m², administered orally twice weekly; 400 mg/m², administered orally twice weekly; 425 mg/m², administered orally twice weekly; 450 mg/m², administered orally twice weekly; 500 mg/m², administered orally twice weekly; 550 mg/m², administered orally twice weekly; 600 mg/m², administered orally twice weekly; 650 mg/m², administered orally twice weekly; 700 mg/m², administered orally twice weekly; 750 mg/m², administered orally twice weekly; 800 mg/m², administered orally twice weekly; 100 mg/m², administered orally every 72 hours; 125 mg/m², administered orally every 72 hours; 150 mg/m², administered orally every 72 hours; 200 mg/m², administered orally every 72 hours; 250 mg/m², administered orally every 72 hours; 275 mg/m², administered orally every 72 hours; 300 mg/m², administered orally every 72 hours; 350 mg/m², administered orally every 72 hours; 400 mg/m², administered orally every 72 hours; 425 mg/m², administered orally every 72 hours; 450 mg/m², administered orally every 72 hours; 500 mg/m², administered orally every 72 hours; 550 mg/m², administered orally every 72 hours; 600 mg/m², administered orally every 72 hours; 650 mg/m², administered orally every 72 hours; 700 mg/m², administered orally every 72 hours; 750 mg/m², administered orally every 72 hours; 800 mg/m², administered orally every 72 hours; 100 mg/m², administered orally every 84 hours; 125 mg/m², administered orally every 84 hours; 150 mg/m², administered orally every 84 hours; 200 mg/m², administered orally every 84 hours; 250 mg/m², administered orally every 84 hours; 275 mg/m², administered orally every 84 hours; 300 mg/m², administered orally every 84 hours; 350 mg/m², administered orally every 84 hours; 400 mg/m², administered orally every 84 hours; 425 mg/m², administered orally every 84 hours; 450 mg/m², administered orally every 84 hours; 500 mg/m², administered orally every 84 hours; 550 mg/m², administered orally every 84 hours; 600 mg/m², administered orally every 84 hours; 650 mg/m², administered orally every 84 hours; 700 mg/m², administered orally every 84 hours; 750 mg/m², administered orally every 84 hours; 800 mg/m², administered orally every 84 hours; 100 mg/m², administered orally every 96 hours; 125 mg/m², administered orally every 96 hours; 150 mg/m², administered orally every 96 hours; 200 mg/m², administered orally every 96 hours; 250 mg/m², administered orally every 96 hours; 275 mg/m², administered orally every 96 hours; 300 mg/m², administered orally every 96 hours; 350 mg/m², administered orally every 96 hours; 400 mg/m², administered orally every 96 hours; 425 mg/m², administered orally every 96 hours; 450 mg/m², administered orally every 96 hours; 500 mg/m², administered orally every 96 hours; 550 mg/m², administered orally every 96 hours; 600 mg/m², administered orally every 96 hours; 650 mg/m², administered orally every 96 hours; 700 mg/m², administered orally every 96 hours; 750 mg/m², administered orally every 96 hours; or 800 mg/m², administered orally every 96 hours.

Minimum and maximum threshold levels of a metabolite depend on a variety of factors, such as the type of subject, metabolite, therapeutic agent, and type of sample. Minimum and maximum threshold levels may be expressed in absolute terms, e.g., in units of concentration, or in relative terms, e.g., in ratios relative to a baseline or reference value. For example, the minimum threshold (below which a patient may receive a dose increase or additional dose) could also be calculated in terms of increase from a pre-treatment DHO level or baseline level.

Minimum threshold levels of DHO or orotate in a human plasma sample may be about 0 ng/ml, about 10 ng/mL, about 20 ng/mL, about 50 ng/mL, about 100 ng/mL, about 150 ng/mL, about 200 ng/mL, about 250 ng/mL, about 300 ng/mL, about 350 ng/mL, about 400 ng/mL, about 450 ng/mL, about 500 ng/mL, about 550 ng/mL, about 600 ng/mL, about 650 ng/mL, about 700 ng/mL, about 750 ng/mL, about 800 ng/mL, about 850 ng/mL, about 900 ng/mL, about 950 ng/mL, about 1000 ng/mL, about 1250 ng/ml, about 1500 ng/ml, about 1750 ng/ml, about 2000 ng/ml, about 2500 ng/ml, about 3000 ng/ml, about 3500 ng/ml, about 4000 ng/ml, about 4500 ng/ml, about 5000 ng/ml, about 6000 ng/ml, about 8000 ng/ml, about 10,000 ng/ml, about 12,000 ng/ml, about 15,000 ng/ml, about 20,000 ng/ml, about 25,000 ng/ml, about 30,000 ng/ml, about 40,000 ng/ml, about 50,000 ng/ml, about 75,000 ng/ml, about 100,000 ng/ml, about 150,000 ng/ml, about 200,000 ng/ml, about 300,000 ng/ml, or about 400,000 ng/ml. The minimum threshold may include any value that falls between the values recited above. Thus, the minimum threshold may include any value between 0 ng/ml and 400.00 ng/ml.

Maximum threshold levels of DHO or orotate in a human plasma sample may be about 50 ng/mL, about 100 ng/mL, about 150 ng/mL, about 200 ng/mL, about 250 ng/mL, about 300 ng/mL, about 350 ng/mL, about 400 ng/mL, about 450 ng/mL, about 500 ng/mL, about 550 ng/mL, about 600 ng/mL, about 650 ng/mL, about 700 ng/mL, about 750 ng/mL, about 800 ng/mL, about 850 ng/mL, about 900 ng/mL, about 950 ng/mL, about 1000 ng/mL, about 1250 ng/ml, about 1500 ng/ml, about 1750 ng/ml, about 2000 ng/ml, about 2500 ng/ml, about 3000 ng/ml, about 3500 ng/ml, about 4000 ng/ml, about 4500 ng/ml, about 5000 ng/ml, about 6000 ng/ml, about 8000 ng/ml, about 10,000 ng/ml, about 12,000 ng/ml, about 15,000 ng/ml, about 20,000 ng/ml, about 25,000 ng/ml, about 30,000 ng/ml, about 40,000 ng/ml, about 50,000 ng/ml, about 75,000 ng/ml, about 100,000 ng/ml, about 150,000 ng/ml, about 200,000 ng/ml, about 300,000 ng/ml, about 400,000 ng/ml, or about 500,000 ng/ml. The maximum threshold may include any value that falls between the values recited above. Thus, the maximum threshold may include any value between 50 ng/ml and 500.00 ng/ml.

The minimum threshold of DHO or orotate may be about 1.5 times the baseline level, about 2 times the baseline level, about 2.5 times the baseline level, about 3 times the baseline level, about 4 times the baseline level, about 5 times the baseline level, about 10 times the baseline level, about 20 times the baseline level, about 50 times the baseline level, about 100 times the baseline level, about 200 times the baseline level, about 500 times the baseline level, about 1000 times the baseline level, about 2000 times the baseline level, or about 5000 times the baseline level. The minimum threshold may include any ratio that falls between those recited above. Thus, the minimum threshold may be any ratio between 1.5 times the baseline level and 5000 times the baseline level.

The maximum threshold of DHO or orotate may be about 2 times the baseline level, about 2.5 times the baseline level, about 3 times the baseline level, about 4 times the baseline level, about 5 times the baseline level, about 10 times the baseline level, about 20 times the baseline level, about 50 times the baseline level, about 100 times the baseline level, about 200 times the baseline level, about 500 times the baseline level, about 1000 times the baseline level, about 2000 times the baseline level, about 5000 times the baseline level, or about 10,000 times the baseline level. The maximum threshold may include any ratio that falls between those recited above. Thus, the maximum threshold may be any ratio between 2 times the baseline level and 10,000 times the baseline level.

The agent may be any agent that alters activity of a metabolic pathway. Preferably, the agent is an inhibitor of an enzyme in a metabolic pathway. Several inhibitors of enzymes in the pyrimidine synthesis pathway are known in the art. Inhibitors of DHODH include brequinar, leflunomide, and teriflunomide. Brequinar, which has the systematic name 6-fluoro-2-(2′-fluoro-1,1′ biphenyl-4-yl)-3-methyl-4-quinoline carboxylic acid, has the following structure:

Brequinar and related compounds are described in, for example, U.S. Pat. Nos. 4,680,299 and 5,523,408, the contents of which are incorporated herein by reference. The use of brequinar to treat leukemia is described in, for example, U.S. Pat. No. 5,032,597 and WO 2017/037022, the contents of which are incorporated herein by reference. Leflunomide, N-(4′-trifluoromethylphenyl)-5-methylisoxazole-4-carboxamide (I), is described in, for example, U.S. Pat. No. 4,284,786, the contents of which are incorporated herein by reference.

Teriflunomide, 2-cyano-3-hydroxy-N-[4-(trifluoromethyl)phenyl]-2-butenamide, is described in, for example, U.S. Pat. No. 5,679,709, the contents of which are incorporated herein by reference. OMP decarboxylase inhibitors include pyrazofurin. Pyrazofurin, 5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1H-pyrazole-3-carboxamide, has the following structure:

Pyrazofurin and related compounds are described in, for example, U.S. Pat. Nos. 3,674,774 and 3,802,999, the contents of which are incorporated herein by reference. ATCase inhibitors include N-(phosphonacetyl)-L-aspartate (PALA). PALA is described in, for example, Swyryd et al, N-(Phosphonacetyl)-L-Aspartate, a Potent Transition State Analog Inhibitor of Aspartate Transcarbamylase, Blocks Proliferation of Mammalian Cells in Culture, J. Biol. Chem. Vol. 249, No. 21, Issue of November 10, pp. 6945-6950, 1974.

Dosing of the agent may account for the formulation of the agent. For example, therapeutic agents, such as brequinar, pyrazofurin, leflunomide, teriflunomide, and PALA, may be provided as prodrugs, analogs, derivatives, or salts. Any of the aforementioned chemical forms may be provided in a pharmaceutically acceptable formulation, such as a micellar formulation.

Dosage of the agent also depends on factors such as the type of subject and route of administration. The dosage may fall within a range for a given type of subject and route of administration, or the dosage may adjusted by a specified amount for a given type of subject and route of administration. For example, dosage of brequinar for oral or intravenous administration to a subject, such as human or mouse, may be about 1 mg/kg, about 2 mg/kg, about 5 mg/kg, about 7.5 mg/kg, about 10 mg/kg, about 15 mg/kg, about 20 mg/kg, about 25 mg/kg, about 50 mg/kg, about 75 mg/kg, or about 100 mg/kg. Dosage of brequinar for oral or intravenous administration to a subject, such as human or mouse, may be adjusted by about 1 mg/kg, about 2 mg/kg, about 5 mg/kg, about 7.5 mg/kg, about 10 mg/kg, about 15 mg/kg, about 20 mg/kg, about 25 mg/kg, or about 50 mg/kg. Dosage of brequinar for oral or intravenous administration to an animal subject, such as a human or mouse, may be about 50 mg/m², about 100 mg/m², about 200 mg/m², about 300 mg/m², about 350 mg/m², about 400 mg/m², about 500 mg/m², about 600 mg/m², about 700 mg/m², about 750 mg/m², about 800 mg/m², or about 1000 mg/m². Dosage of brequinar for oral or intravenous administration to an animal subject, such as a human or mouse, may be adjusted by about 50 mg/m², about 100 mg/m², about 200 mg/m², about 300 mg/m², about 350 mg/m², or about 400 mg/m².

FIG. 1A through FIG. 1C are a series of graphs showing levels of brequinar and DHO in three patients that have received a single dose of brequinar according to the same dosing regimen. The graph on the left is from patient #1, the graph in center is from patient #2, and the graph on the right is from patient #3. Levels of brequinar are shown in dark green, and levels of DHO are shown in red. Metabolism of brequinar is faster than average in patient #1, average in patient #2, and slower than average in patient #3. Inhibition of DHODH leads to accumulation of DHO, a substrate of DHODH. However, analysis of brequinar levels alone provides an incomplete picture of the efficacy of brequinar. Because analysis of DHO levels gives a more accurate representation of target engagement, DHO is a superior biomarker.

FIG. 2A through FIG. 2L are a series of graphs showing levels of brequinar and DHO in three patients that have received a multiple doses of brequinar according to the same dosing regimen. The graph on the top is from patient #2, the graph in center is from patient #1, and the graph on the bottom is from patient #3. Levels of brequinar are shown in dark green, levels of DHO are shown in red, and the dashed line represents a threshold level above which brequinar provides sufficient inhibition of DHODH. In patient #2, i.e., a patient with an average rate of brequinar metabolism, the dosing regimen provides periods of sustained inhibition of DHODH interspersed with short recovery periods. This dosing regimen is optimal for patient #2 because the prolonged inhibition of DHODH kills leukemia cells that are sensitive to uridine starvation, while the recovery period allows an adequate supply of pyrimidines to support survival of normal cells. In patient #1, however, the duration of DHODH inhibition is not sufficient to kill leukemia cells, so this dosing regimen does not provide a therapeutic benefit. Conversely, in patient #3, the second and subsequent doses of brequinar are provided too shortly after DHODH activity is restored following the previous dose, and the pyrimidine pool is not adequately restored to support survival of normal cells. Consequently, this dosing regimen is toxic to patient #3.

FIG. 3 is a flow chart illustrating an example of determining a dose a of DHODH inhibitor for a patient according to an embodiment of the invention. A pre-treatment DHO level is measured to determine the DHO baseline for the patient. The patient is given a starting dose for 2 weeks and examined for the presence of adverse events (AE). If adverse events occur, subsequent doses are withheld to see whether the adverse events resolve within 7 days. If adverse events resolve, dosage is decreased by 75 mg/m² and dosing is resumed. If no adverse events occur, DHO levels are analyzed at 84 hours post-administration. If DHO levels are below 100 ng/mL or two times the baseline, dosage of brequinar is increased by 150 mg/m² but not to exceed a maximum dosage of 800 mg/m². If DHO levels are above 100 ng/mL, the dosing is maintained for 2 weeks. The process can be repeated to optimize the dosing to achieve sustained elevation of DHO levels above the threshold level without adverse events.

The methods are useful for providing guidance on dosing of therapeutic agents for individuals. Therefore, the methods may be performed by any party that wishes to provide such guidance. For example and without limitation, the methods may be performed by a clinical laboratory; a physician or other medical professional; a supplier or manufacturer of a therapeutic agent; an organization that provides analytical services to a physician, clinic, hospital, or other medical service provider; or a healthcare consultant.

Disorders that can be Treated by Altering Activity of a Metabolic Pathway

The methods of the invention are useful for determining the dosage of drugs that affect that alter the activity of a metabolic pathway to treat or prevent a disorder. Preferably, the drug inhibits an enzyme in the metabolic pathway. In other embodiments, the drug inhibits an enzyme in a related metabolic pathway, such as a pathway that regulates, compensates for, or antagonizes the pathway in which the target enzyme functions. Thus, the disorder may be any disease, disorder, or condition for which enzyme inhibition provides a therapeutic benefit.

For example and without limitation, one disorder that can be treated by methods of the invention is acute myeloid leukemia (AML). In AML, myeloblasts arrested in an early stage of differentiation proliferate in an uncontrolled manner and interfere with the development of other blood cells in the bone marrow. Inhibitors of dihydroorotate dehydrogenase (DHODH), an enzyme involved in pyrimidine synthesis, cause differentiation of myeloblasts and prevent their leukemia-initiating activity. The role of DHODH in AML is described in Sykes et al., Inhibition of Dihydroorotate Dehydrogenase Overcomes Differentiation Blockade in Acute Myeloid Leukemia, Cell 167, 171-186, Sep. 22, 2016; dx.doi.org/10.1016/j.cell.2016.08.057, the contents of which are incorporate herein by reference.

The use of DHODH inhibitors to treat AML requires a precise dosing regimen. Care must be taken to avoid excessive inhibition of DHODH. DHODH is an essential enzyme, and homozygous recessive mutations in DHODH cause Miller syndrome, a disorder characterized by multi-organ dysfunction. In a mouse model of AML, daily administration of high doses of the DHODH inhibitor brequinar lead to weight loss, anemia, and thrombocytopenia. At the same time, sustained exposure to brequinar is necessary to inhibit DHODH for sufficient periods to produce a therapeutic effect in the mouse AML model. Without wishing to be bound by theory, one hypothesis for the narrow therapeutic window of brequinar in treating AML in both the mouse model and in humans is that malignant cells display an increased sensitivity to DHODH inhibition. In particular, normal cells may be able to tolerate periods of nucleotide starvation that kill cancer cells due to the elevated metabolic needs of the latter.

The narrow therapeutic window of DHODH inhibition likely applies to other disorders as well. For example, brequinar was evaluated for treatment of solid tumor malignancies and found to be ineffective when administered over a 5-day period followed by a 3-week gap or once per week for three weeks followed by a 1-week gap. See Arteaga, C. L. et al. (1989) Phase I clinical and pharmacokinetic trial of Brequinar sodium (DuP 785; NSC 368390) Cancer Res. 49, 4648-4653; Burris, H. A., et al. (1998) Pharmacokinetic and phase I studies of brequinar (DUP 785; NSC 368390) in combination with cisplatin in patients with advanced malignancies, Invest. New Drugs 16, 19-27; Noe, D. A., et al. (1990) Phase I and pharmacokinetic study of brequinar sodium (NSC 368390), Cancer Res. 50, 4595-4599; Schwartsmann, G. et al. (1990) Phase I study of Brequinar sodium (NSC 368390) in patients with solid malignancies, Cancer Chemother. Pharmacol. 25, 345-351, the contents of each of which are incorporated herein by reference. However, brequinar may be effective for treatment of other cancers if the drug is administered in a manner that provides sustained DHODH inhibition.

It is understood that the aforementioned examples are provided for illustrative purposes only and that the methods of the invention can be used for treatment of any disorder or disease in which the measured level of a metabolite can be used to assess target engagement. The disorder may be one in which inhibiting an enzyme in a metabolic pathway is of therapeutic benefit. The disorder may be cancer. The cancer may include a solid tumor or hematological tumor. The cancer may be acute lymphoblastic leukemia (ALL), adult T cell leukemia/lymphoma (ATLL), bladder cancer, breast cancer, such as triple negative breast cancer (TNBC), glioma, head and neck cancer, leukemia, such as AML, lung cancer, such as small cell lung cancer and non-small cell lung cancer, lymphoma, multiple myeloma, neuroblastoma, osteosarcoma, ovarian cancer, prostate cancer, or renal cell cancer. The disorder may have a genetic mutation such as MYC amplification or PTEN loss that leads to increased dependence on the metabolic pathway, such as increased “addiction” to glutamine. The disorder may be an inflammatory or autoimmune disorder, such as arthritis, hepatitis, chronic obstructive pulmonary disease, multiple sclerosis, or tendonitis. The disorder may be a psychiatric disorder, such as anxiety, stress, obsessive-compulsive disorder, depression, panic disorder, psychosis, addiction, alcoholism, attention deficit hyperactivity, agoraphobia, schizophrenia, or social phobia. The disorder may be a neurological or pain disorder, such as epilepsy, stroke, insomnia, diskinesia, peripheral neuropathic pain, chronic nociceptive pain, phantom pain, deafferentation pain, inflammatory pain, joint pain, wound pain, post-surgical pain, or recurrent headache pain, appetite disorders, or motor activity disorders. The disorder may be a neurodegenerative disorder, such as Alzheimer's disease, Parkinson's disease, or Huntington's disease.

The methods of the invention may be used to treat brain cancer. Brain tumors may be classified as primary, i.e., originating in the brain or secondary, i.e., originating in other organs and metastasizing into the brain. A commonly used scheme for classification of tumors of the central nervous system (CNS) is provided by the World Health Organization (WHO) and described in, for example, Louis D N, et al., (August 2007) “The 2007 WHO Classification of Tumours of the Central Nervous System”. Acta Neuropathol. 114 (2): 97-109, doi:10.1007/s00401-007-0243-4. PMC 1929165, PMID 17618441; and Louis D N, et al., (eds) (2007). World Health Organization Classification of Tumours of the Central Nervous System. IARC, Lyon ISBN 92-832-2430-2, the contents of each of which are incorporated herein by reference. Under the WHO classification scheme, CNS tumors includes tumors of neuroepithelial tissue, such as astrocytic tumors (astrocytomas), oligodendroglial tumors, oligoastrocytic tumors, ependymal tumors, choroid plexus tumors, other neuroepithelial tumors, neuronal and mixed neuronal-glial tumors, tumors of the pineal region, and embryonal tumors, including neuroblastoma; tumors of cranial and paraspinal nerves, such as schwannoma, neurofibroma, perineurioma, and malignant peripheral nerve sheath tumors; tumors of the meninges, such as tumors of meningothelial cells, mesenchymal tumors, rimary melanocytic lesions, and other neoplasms related to the meninges; tumors of the hematopoietic system, such as malignant lymphomas, plasmacytoma, and granulocytic sarcoma; germ cell tumors, such as germinoma, embryonal carcinoma, yolk sac tumor, choriocarcinoma, teratoma, and mixed germ cell tumors; tumors of the sellar region, such as craniopharyngioma, granular cell tumor, pituicytoma, and spindle cell oncocytoma of the adenohypophysis; and metastatic tumors from other tissues, such as lung, breast, melanoma, kidney, and colorectal tissue. In some embodiments, the methods of the invention are used to treat tumors derived from neuroepithelial cells. In some embodiments, the methods of the invention are used to treat astrocytoma, glioma, meningioma, or neuroblastoma. The brain cancer may be associated with a genetic mutation such as MYC amplification or PTEN loss that leads to increased dependence on the metabolic pathway, such as increased “addiction” to glutamine.

The disorder may include a class or subset of patients having a disease, disorder, or condition. For example, AML cases are classified based on cytological, genetic, and other criteria, and AML treatment strategies vary depending on classification. One AML classification system is provided by the World Health Organization (WHO). The WHO classification system includes subtypes of AML provided in Table 1 and is described in Falini B, et al. (October 2010) “New classification of acute myeloid leukemia and precursor-related neoplasms: changes and unsolved issues” Discov Med. 10 (53): 281-92, PMID 21034669, the contents of which are incorporated herein by reference.

TABLE 1 Name Description Acute myeloid Includes: leukemia with AML with translocations between chromosome 8 and 21 - recurrent [t(8; 21)(q22; q22);] RUNX1/RUNX1T1; (ICD-O 9896/3); genetic AML with inversions in chromosome 16 - [inv(16)(p13.1q22)] or internal abnormalities translocations in it - [t(16; 16)(p13.1; q22);] CBFB/MYH11; (ICD-O 9871/3); Acute promyelocytic leukemia with translocations between chromosome 15 and 17 - [t(15; 17)(q22; q12);] RARA/PML; (ICD-O 9866/3); AML with translocations between chromosome 9 and 11 - [t(9; 11)(p22; q23);] MLLT3/MLL; AML with translocations between chromosome 6 and 9 - [t(6; 9)(p23; q34);] DEK/NUP214; AML with inversions in chromosome 3 - [inv(3)(q21q26.2)] or internal translocations in it - [t(3; 3)(q21; q26.2);] RPN1/EVI1; Megakaryoblastic AML with translocations between chromosome 1 and 22 - [t(1; 22)(p13; q13);] RBM15/MKL1; AML with mutated NPM1 AML with mutated CEBPA AML with Includes people who have had a prior documented myelodysplastic myelodysplasia- syndrome (MDS) or myeloproliferative disease (MPD) that then has related changes transformed into AML, or who have cytogenetic abnormalities characteristic for this type of AML (with previous history of MDS or MPD that has gone unnoticed in the past, but the cytogenetics is still suggestive of MDS/MPD history). This category of AML occurs most often in elderly people and often has a worse prognosis. Includes: AML with complex karyotype Unbalanced abnormalities AML with deletions of chromosome 7 - [del(7q);] AML with deletions of chromosome 5 - [del(5q);] AML with unbalanced chromosomal aberrations in chromosome 17 - [i(17q)/t(17p);] AML with deletions of chromosome 13 - [del(13q);] AML with deletions of chromosome 11 - [del(11q);] AML with unbalanced chromosomal aberrations in chromosome 12 - [del(12p)/t(12p);] AML with deletions of chromosome 9 - [del(9q);] AML with aberrations in chromosome X - [idic(X)(q13);] Balanced abnormalities AML with translocations between chromosome 11 and 16 - [t(11; 16)(q23; q13.3);], unrelated to previous chemotherapy or ionizing radiation AML with translocations between chromosome 3 and 21 - [t(3; 21)(q26.2; q22.1);], unrelated to previous chemotherapy or ionizing radiation AML with translocations between chromosome 1 and 3 - [t(1; 3)(p36.3; q21.1);] AML with translocations between chromosome 2 and 11 - [t(2; 11)(p21; q23);], unrelated to previous chemotherapy or ionizing radiation AML with translocations between chromosome 5 and 12 - [t(5; 12)(q33; p12);] AML with translocations between chromosome 5 and 7 - [t(5; 7)(q33; q11.2);] AML with translocations between chromosome 5 and 17 - [t(5; 17)(q33; p13);] AML with translocations between chromosome 5 and 10 - [t(5; 10)(q33; q21);] AML with translocations between chromosome 3 and 5 - [t(3; 5)(q25; q34);] Therapy-related Includes people who have had prior chemotherapy and/or radiation and myeloid subsequently develop AML or MDS. These leukemias may be characterized neoplasms by specific chromosomal abnormalities, and often carry a worse prognosis. Myeloid Includes myeloid sarcoma. sarcoma Myeloid Includes so-called “transient abnormal myelopoiesis” and “Myeloid leukemia proliferations associated with Down syndrome” related to Down syndrome Blastic Includes so-called “blastic plasmacytoid dendritic cell neoplasm” plasmacytoid dendritic cell neoplasm AML not Includes subtypes of AML that do not fall into the above categories otherwise AML with minimal differentiation categorized AML without maturation AML with maturation Acute myelomonocytic leukemia Acute monoblastic and monocytic leukemia Acute erythroid leukemia Acute megakaryoblastic leukemia Acute basophilic leukemia Acute panmyelosis with myelofibrosis

An alternative classification scheme for AML is the French-American-British (FAB) classification system. The FAB classification system includes the subtypes of AML provided in Table 2 and is described in Bennett J M, et al. (August 1976). “Proposals for the classification of the acute leukaemias. French-American-British (FAB) co-operative group” Br. J. Haematol. 33 (4): 451-8, doi:10.1111/j.1365-2141.1976.tb03563.x. PMID 188440; and Bennett J M, et al. (June 1989) “Proposals for the classification of chronic (mature) B and T lymphoid leukaemias. French-American-British (FAB) Cooperative Group” J. Clin. Pathol. 42 (6): 567-84, doi:10.1136/jcp.42.6.567, PMC 1141984, PMID 2738163, the contents of each of which are incorporated herein by reference.

TABLE 2 Type Name Cytogenetics M0 acute myeloblastic leukemia, minimally differentiated M1 acute myeloblastic leukemia, without maturation M2 acute myeloblastic leukemia, with t(8; 21)(q22; q22), granulocytic maturation t(6; 9) M3 promyelocytic, or acute promyelocytic t(15; 17) leukemia (APL) M4 acute myelomonocytic leukemia inv(16)(p13q22), del(16q) M4eo myelomonocytic together with bone inv(16), t(16; 16) marrow eosinophilia M5 acute monoblastic leukemia (M5a) or del (11q), t(9; 11), acute monocytic leukemia (M5b) t(11; 19) M6 acute erythroid leukemias, including erythroleukemia (M6a) and very rare pure erythroid leukemia (M6b) M7 acute megakaryoblastic leukemia t(1; 22)

The disorder may include a sub-population of patients. For example, the patients may be pediatric, newborn, neonates, infants, children, adolescent, pre-teens, teenagers, adults, or elderly. The patients may be in critical care, intensive care, neonatal intensive care, pediatric intensive care, coronary care, cardiothoracic care, surgical intensive care, medical intensive care, long-term intensive care, an operating room, an ambulance, a field hospital, or an out-of-hospital field setting.

Providing Doses of a Therapeutic Agent

Methods of the invention may include providing a therapeutic agent to a subject according to a dosing regimen or dosage determined as described above. Providing the agent to the subject may include administering it to the subject. A dose may be administered as a single unit or in multiple units. The agent may be administered by any suitable means. For example and without limitation, the agent may be administered orally, intravenously, enterally, parenterally, dermally, buccally, topically, transdermally, by injection, intravenously, subcutaneously, nasally, pulmonarily, or with or on an implantable medical device (e.g., stent or drug-eluting stent or balloon equivalents).

In some embodiments, the methods include assessing a metabolite level in a sample from a subject, and determining whether that level is within a threshold range (e.g., above a minimal threshold and/or below a potential toxicity threshold) that warrants dosing, and/or that warrants dosing at a particular level or in a particular amount.

The methods may include administering at least one dose of the agent to a subject whose plasma metabolite level has been determined and is below a pre-determined threshold (e.g., a pre-determined potential toxicity threshold and/or a pre-determined potential efficacy threshold). In some embodiments, the predetermined threshold reflects percent inhibition of a target enzyme in the subject relative to a baseline determined for the subject. In some embodiments, the baseline is determined by an assay.

For example, in some embodiments, in order to maintain inhibition of the target enzyme at an effective threshold, multiple doses of the agent may be administered. In some embodiments, dosing of the agent can occur at different times and in different amounts. The present disclosure encompasses those methods that can maintain inhibition of the target enzyme at a consistent level at or above the efficacy threshold throughout the course of treatment. In some embodiments, the amount of inhibition of the target enzyme is measured by the amount of metabolite in the plasma of a subject.

In some embodiments, more than one dose of the agent is administered to the subject. In some embodiments, the method further comprises a step of re-determining the subject's plasma metabolite level after administration of the at least one dose. In some embodiments, the subject's plasma metabolite level is re-determined after each dose. In some embodiments, the method further comprises administering at least one further dose of the agent after the subject's plasma metabolite level has been determined again (e.g., after administering a first or previous dose), and is below the pre-determined threshold. If the subject's plasma metabolite level is determined to be above a pre-determined threshold, dosing can be discontinued. In some embodiments, therefore, no further dose of the agent is administered until the subject's plasma metabolite level has been determined to again be below a pre-determined threshold.

The methods may include administering an agent to a subject at a dosage level at or near a cell-lethal level. Such dosage can be supplemented with a later dose at a reduced level, or by discontinuing of dosing. For example, in some embodiments, the present disclosure provides a method of administering a dihydroorotate dehydrogenase inhibitor to a subject in need thereof, the method comprising: administering a plurality of doses of an agent, according to a regimen characterized by at least first and second phases, wherein the first phase involves administration of at least one bolus dose of an agent at a cell-lethal level; and the second phase involves either: administration of at least one dose that is lower than the bolus dose; or absence of administration of an agent.

In some embodiments, an agent is not administered during a second phase. In some embodiments, a second phase involves administration of uridine rescue therapy. In some embodiments, a bolus dose is or comprises a cell lethal dose. In some embodiments, a cell lethal dose is an amount of an agent that is sufficient to cause apoptosis in normal (e.g., non-cancerous) cells in addition to target cells (e.g., cancer cells).

In some embodiments, the first phase and the second phase each comprise administering an agent. In some embodiments, the first phase and the second phase are at different times. In some embodiments, the first phase and the second phase are on different days. In some embodiments, the first phase lasts for a period of time that is less than four days. In some embodiments, the first phase comprises administering an agent, followed by a period of time in which no agent is administered. In some embodiments, the period of time in which no agent is administered is 3 to 7 days after the dose during the first phase. In some embodiments, the first phase comprises administering more than one dose.

In some embodiments, an agent is administered during a second phase. In some embodiments, an agent is administered sub-cell-lethal levels during the second phase. In some embodiments, the first phase is repeated after the second phase. In some embodiments, both the first and second phases are repeated.

In some embodiments, the present disclosure provides a method of administering an agent to a subject in need thereof, according to a multi-phase protocol comprising: a first phase in which at least one dose of the agent is administered to the subject; and a second phase in which at least one dose of the agent is administered to the subject, wherein one or more doses administered in the second phase differs in amount and/or timing relative to other doses in its phase as compared with the dose(s) administered in the first phase.

In some embodiments, a metabolite level is determined in a sample from the subject between the first and second phases. In some embodiments, the sample is a plasma sample. In some embodiments, the timing or amount of at least one dose administered after the metabolite level is determined or differs from that of at least one dose administered before the metabolite level was determined.

In some embodiments, the amount of agent that is administered to the patient is adjusted in view of the metabolite level in the subject's plasma. For example, in some embodiments, a first dose is administered in the first phase. In some embodiments, metabolite level is determined at a period of time after administration of the first dose.

In some embodiments, if the metabolite level is below a pre-determined level, the amount of agent administered in a second or subsequent dose is increased and/or the interval between doses is reduced. For example, in some such embodiments, the amount of agent administered may be increased, for example, by 100 mg/m². In some embodiments, the amount of agent administered in a second or subsequent dose is increased by 150 mg/m². In some embodiments, the amount of agent administered in a second or subsequent dose is increased by 200 mg/m². In some embodiments, the amount of agent administered may be increased by an adjustment amount determined based on change in metabolite levels observed between prior doses of different amounts administered to the subject.

In some embodiments, if the metabolite level is above a pre-determined level, the amount of agent administered in a second or subsequent dose is the same as the amount administered in the first or previous dose and/or the interval between doses is the same.

In some embodiments, if the metabolite level is above a pre-determined level, the amount of agent in a second or subsequent dose is decreased and/or the interval between doses is increased. For example, in some such embodiments, the amount of agent administered may be decreased, for example, by 50 mg/m². In some embodiments, if the metabolite level is above a pre-determined level, the amount of agent in a second or subsequent dose is decreased by 75 mg/m². In some embodiments, if the metabolite level is above a pre-determined level, the amount of agent in a second or subsequent dose is decreased by 100 mg/m². In some embodiments, the amount of agent administered may be decreased by an adjustment amount determined based on change in metabolite levels observed between prior doses of different amounts administered to the subject.

In some embodiments, the present disclosure provides a method of administering a later dose of an agent to a patient who has previously received an earlier dose of the agent, wherein the patient has had a level of metabolite assessed subsequent to administration of the earlier dose, and wherein the later dose is different than the earlier dose. The later dose may be different from the earlier dose in amount of agent included in the dose, time interval relative to an immediately prior or immediately subsequent dose, or combinations thereof. The amount of agent in the later dose may be less than that in the earlier dose.

The method may include administering multiple dose of the agent, separated from one another by a time period that is longer than 2 days and shorter than 8 days For example, the time period may be about 3 days.

In some embodiments, the metabolite level is determined in a sample from the subject before each dose is administered, and dosing is delayed or skipped if the determined metabolite level is above a pre-determined threshold. For example, the metabolite level may be determined about 12 hours, about 24 hours, about 36 hours, about 48 hours, about 60 hours, about 72 hours, about 84 hours, or about 96 hours after administration of an agent

The method may include administering the agent according to a regimen approved in a trial in which a level of metabolite was measured in a patients between doses of the agent The regimen may include multiple doses whose amount and timing were determined in the trial to maintain the metabolite level within a range determined to indicate a degree of target enzyme inhibition below a toxic threshold and above a minimum threshold. The regimen may include determining the metabolite level in the subject after administration of one or more doses of the agent.

In some embodiments, the regimen includes a dosing cycle in which an established pattern of doses is administered over a first period of time. In some embodiments, the regimen comprises a plurality of the dosing cycles. In some embodiments, the regimen includes a rest period during which the agent is not administered between the cycles.

Compositions Containing DHODH Inhibitors

The compositions of the invention include DHODH inhibitors. Several DHODH inhibitors are known in the art. For example, inhibitors of DHODH include brequinar, leflunomide, and teriflunomide. Brequinar, which has the systematic name 6-fluoro-2-(2′-fluoro-1,1′ biphenyl-4-yl)-3-methyl-4-quinoline carboxylic acid, has the following structure:

Brequinar and related compounds are described in, for example, U.S. Pat. Nos. 4,680,299 and 5,523,408, the contents of which are incorporated herein by reference. The use of brequinar to treat leukemia is described in, for example, U.S. Pat. No. 5,032,597 and WO 2017/037022, the contents of which are incorporated herein by reference. Leflunomide, N-(4′-trifluoromethylphenyl)-5-methylisoxazole-4-carboxamide (I), is described in, for example, U.S. Pat. No. 4,284,786, the contents of which are incorporated herein by reference. Teriflunomide, 2-cyano-3-hydroxy-N-[4-(trifluoromethyl)phenyl]-2-butenamide, is described in, for example, U.S. Pat. No. 5,679,709, the contents of which are incorporated herein by reference.

The DHODH inhibitor may be provided as a prodrug, analog, derivative, or salt. The DHODH inhibitor may be provided in a micellar formulation.

The DHODH inhibitors, including prodrugs, analogs, derivatives, and salts thereof, may be provided as pharmaceutical compositions. A pharmaceutical composition may be in a form suitable for oral use, for example, as tablets, troches, lozenges, fast-melts, aqueous or oily suspensions, dispersible powders or granules, emulsions, hard or soft capsules, syrups or elixirs. Compositions intended for oral use may be prepared according to any method known in the art for the manufacture of pharmaceutical compositions and such compositions may contain one or more agents selected from sweetening agents, flavoring agents, coloring agents and preserving agents, in order to provide pharmaceutically elegant and palatable preparations. Tablets contain the compounds in admixture with non-toxic pharmaceutically acceptable excipients which are suitable for the manufacture of tablets. These excipients may be, for example, inert diluents, such as calcium carbonate, sodium carbonate, lactose, calcium phosphate or sodium phosphate; granulating and disintegrating agents, for example corn starch, or alginic acid; binding agents, for example starch, gelatin or acacia, and lubricating agents, for example magnesium stearate, stearic acid or talc.

The tablets may be uncoated, or they may be coated by known techniques to delay disintegration in the stomach and absorption lower down in the gastrointestinal tract and thereby provide a sustained action over a longer period. For example, a time delay material such as glyceryl monostearate or glyceryl distearate may be employed. They may also be coated by the techniques described in U.S. Pat. Nos. 4,256,108, 4,166,452 and 4,265,874, to form osmotic therapeutic tablets for control release. Preparation and administration of compounds is discussed in U.S. Pat. No. 6,214,841 and U.S. Pub. No. 2003/0232877, the contents of each of which are incorporated by reference herein.

Formulations for oral use may also be presented as hard gelatin capsules in which the compounds are mixed with an inert solid diluent, for example calcium carbonate, calcium phosphate or kaolin, or as soft gelatin capsules in which the compounds are mixed with water or an oil medium, for example peanut oil, liquid paraffin or olive oil.

An alternative oral formulation, where control of gastrointestinal tract hydrolysis of the compound is sought, can be achieved using a controlled-release formulation, where a compound of the invention is encapsulated in an enteric coating.

Aqueous suspensions may contain the compounds in admixture with excipients suitable for the manufacture of aqueous suspensions. Such excipients are suspending agents, for example sodium carboxymethylcellulose, methylcellulose, hydroxypropylmethylcellulose, sodium alginate, polyvinylpyrrolidone, gum tragacanth and gum acacia; dispersing or wetting agents such as a naturally occurring phosphatide, for example lecithin, or condensation products of an alkylene oxide with fatty acids, for example, polyoxyethylene stearate, or condensation products of ethylene oxide with long chain aliphatic alcohols, for example heptadecaethyleneoxycetanol, or condensation products of ethylene oxide with partial esters derived from fatty acids and a hexitol such a polyoxyethylene with partial esters derived from fatty acids and hexitol anhydrides, for example polyoxyethylene sorbitan monooleate. The aqueous suspensions may also contain one or more preservatives, for example ethyl, or n-propyl p-hydroxybenzoate, one or more coloring agents, one or more flavoring agents, and one or more sweetening agents, such as sucrose or saccharin.

Oily suspensions may be formulated by suspending the compounds in a vegetable oil, for example, arachis oil, olive oil, sesame oil or coconut oil, or in a mineral oil such as liquid paraffin. The oily suspensions may contain a thickening agent, for example beeswax, hard paraffin or cetyl alcohol. Sweetening agents such as those set forth above, and flavoring agents may be added to provide a palatable oral preparation. These compositions may be preserved by the addition of an anti-oxidant such as ascorbic acid.

Dispersible powders and granules suitable for preparation of an aqueous suspension by the addition of water provide the compounds in admixture with a dispersing or wetting agent, suspending agent and one or more preservatives. Suitable dispersing or wetting agents and suspending agents are exemplified, for example sweetening, flavoring and coloring agents, may also be present.

The pharmaceutical compositions may also be in the form of oil-in-water emulsions. The oily phase may be a vegetable oil, for example olive oil or arachis oil, or a mineral oil, for example liquid paraffin or mixtures of these. Suitable emulsifying agents may be naturally-occurring gums, for example gum acacia or gum tragacanth, naturally occurring phosphatides, for example soya bean, lecithin, and esters or partial esters derived from fatty acids and hexitol anhydrides, for example sorbitan monooleate and condensation products of the said partial esters with ethylene oxide, for example polyoxyethylene sorbitan monooleate. The emulsions may also contain sweetening and flavoring agents.

Syrups and elixirs may be formulated with sweetening agents, such as glycerol, propylene glycol, sorbitol or sucrose. Such formulations may also contain a demulcent, a preservative, and agents for flavoring and/or coloring. The pharmaceutical compositions may be in the form of a sterile injectable aqueous or oleaginous suspension. This suspension may be formulated according to the known art using those suitable dispersing or wetting agents and suspending agents which have been mentioned above. The sterile injectable preparation may also be in a sterile injectable solution or suspension in a non-toxic parenterally acceptable diluent or solvent, for example as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil may be employed including synthetic mono- or di-glycerides. In addition, fatty acids such as oleic acid find use in the preparation of injectables.

Pharmaceutical compositions may include other pharmaceutically acceptable carriers, such as sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients, such as cocoa butter and suppository waxes; oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; glycols, such as propylene glycol; polyols, such as glycerin (glycerol), erythritol, xylitol. sorbitol, mannitol and polyethylene glycol; esters, such asethyl oleate and ethyllaurate; agar; buffering agents, such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol; pH buffered solutions; polyesters, polycarbonates and/or polyanhydrides; and other non-toxic compatible substances employed in pharmaceutical formulations. The pharmaceutically acceptable carrier may be an encapsulation coating. For example, the encapsulation coating may contain carrageenan, cellulose acetate phthalate, cellulose acetate succinate, cellulose acetate trimellitate, collagen, gelatin, hydroxypropyl methyl cellulose acetate, a methyl acrylate-methacrylic acid copolymer, polyvinyl acetate phthalate shellac, sodium alginate, starch, or zein.

The N-acylethanolamide compounds, including prodrugs, analogs, and derivatives thereof, may be provided as pharmaceutically acceptable salts, such as nontoxic acid addition salts, which are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange. In some embodiments, pharmaceutically acceptable salts include, but are not limited to, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphor sulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Other pharmaceutically acceptable salts may be found in, for example, Remington, The Science and Practice of Pharmacy (20th ed. 2000). Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. In some embodiments, a pharmaceutically acceptable salt is an alkali salt. In some embodiments, a pharmaceutically acceptable salt is a sodium salt. In some embodiments, a pharmaceutically acceptable salt is an alkaline earth metal salt. In some embodiments, pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counter ions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, alkyl having from 1 to 6 carbon atoms, sulfonate and aryl sulfonate.

Synthesis of Brequinar and Related Compounds

The invention provides methods of making a 2-(2′-halo-1-1′-biphenyl-4-yl)-quinoline carboxylic acid, such as brequinar. The methods include incubating a compound of formula (I) with a compound of formula (II) in a mixture containing a base and adding an acid to the mixture, thereby creating a compound of formula (III) according to following reaction:

in which:

R₁, R₂, R₃, and R₄ are independently H, F, Cl, Br, I, CH₃, CF₃, SCH₃ or CH₂ CH₃, at least two of R₁, R², R₃, and R₄ being H;

R₅ is H, alkoxy of 1-3 carbon atoms, or alkyl of 1-2 carbon atoms;

R₆ and R₇ are independently H, F, Cl, Br, alkyl of 1-5 carbon atoms, NO₂, OH, CF₃ or OCH₃;

X is a halogen; and

the incubating step includes at least one of:

-   -   incubating the mixture at a temperature of from about 60° C. to         about 70° C.,     -   the mixture containing a molar ratio of the base to the compound         of formula (II) of from about 5:1 to about 8:1, and incubating         the mixture for from about 15 hours to about 30 hours.

An insight of the invention is that optimizing the conditions of the first step, i.e., incubating compounds of formula (I) and formula (II) in the presence of a base, improves yield of the product. One key variable is the molar ratio of the base to the compound of formula (II). Higher yields are achieved with when this molar ratio is optimized. For example, the molar ratio of the base to the compound of formula (II) may be from about 5:1 to about 8:1, from about 6.5:1 to about 7.5:1, or about 7:1.

Any suitable base may be used. Preferably, the base is KOH, NaOH, and NH₄OH.

Any suitable alcohol may be used. For example, the alcohol may be methanol, ethanol, 1-propanol, 2-propanol, butanol, 2-methyl-1-propanol, or pentanol.

Another important variable in the incubation step is the temperature. A minimum temperature is required for the reaction to occur, but temperatures that are too high result in increased generation of undesired side products. Thus, the temperature may be from about 60° C. to about 70° C., from about 60° C. to about 65° C., or about 60° C.

Another important variable in the incubation step is the duration. A minimum time is required for the reaction to occur, but excessive incubation time results in the generation of undesired side products. Thus, the length of incubation may be from about 15 hours to about 30 hours, from about 15 hours to about 25 hours, or from about 15 hours to about 20 hours.

The reaction outlined above can be performed using one or more of an optimized molar ratio of the base to the compound of formula (II) as described above, an optimized temperature as described above, and an optimized incubation time as described above. Thus, the reaction may include one, two, or three of the optimized variables described above.

For the acid addition step, the acid may be any suitable acid. For example, the acid may be HCl or acetic acid.

The method may provide a minimum yield of the compound of formula (III). For example, the yield of the compound of formula (III) may be at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%.

The compound of formula (III) may be brequinar. The compound of formula (III) may have the structure represented by formula (IV):

Assessing Tumor Properties

The invention also provides methods for assessing the effects of therapeutic agents on tumors in vivo in real time. This information obtained from such in vivo analysis may be used to determine or make adjustments to dosing regimens.

One modality for assessing the effect of an agent on a tumor is to monitor within the tumor the flux of a metabolite through a pathway whose activity is altered by the agent, such as the pathways and agents described above. Activity of metabolic pathways in vivo can be analyzed in real-time by hyperpolarization magnetic resonance imaging, as described in, for example, Miloushev, V Z et al., Hyperpolarization MRI: Preclinical Models and Potential Applications in Neuroradiology, Top Magn Reson Imaging 2016 February; 25(1): 31-37, doi: 10.1097/RMR.0000000000000076, PMID: 26848559; and Di Gialleonardo, D, et al., The Potential of Metabolic Imaging, Semin Nucl Med. 2016 January; 46(1): 28-39, doi: 10.1053/j.semnuclmed.2015.09.004, PMID: 26687855; and Cho, et al., Noninvasive Interrogation of Cancer Metabolism with Hyperpolarized ¹³C MRI J Nucl Med 2017; 58:1201-1206, DOI: 10.2967/jnumed.116.182170, the contents of each of which are incorporated herein by reference.

Briefly, the methods entail injection of an isotopically-labeled metabolite, which can be imaged by magnetic resonance, into a subject and tracking movement of the isotope through the body. The metabolite may be a carbon-containing molecule, such as an intermediate in the pyrimidine synthesis pathway, that is enriched for an isotope of carbon, such as ¹³C, or nitrogen, such as ¹⁵N. The therapeutic agent may be an agent that inhibits an enzyme in a pathway through which the metabolite passes. Analysis may include comparison of metabolism of the labeled metabolite when the subject has been provided the therapeutic agent with metabolism in an untreated subject, either the same subject or a different subject having similar characteristics. The methods are useful for analysis of tumors due to the increase flux through certain metabolic pathways, such as the pyrimidine synthesis pathway, in tumor cells. For example, a subject having a tumor with increased glutamine flux (determined by isotopically-labeled glutamine) may be given a DHODH inhibitor, e.g., brequinar, and isotopically-labeled DHO. If the level of DHODH inhibition is high, accumulation of the metabolite can be detected at the site of the tumor.

Another way to assess the effect of an agent on a tumor in vivo in real time is to analyze oxygenation of the tumor. Many solid tumors contain regions of poor oxygenation due to the inability of the vasculature to keep pace with the rapid growth of tumor cells. To continue to proliferating when the blood supply is inadequate, tumor cells often alter their metabolism to derive more energy from glucose metabolism and become less dependent on oxygen. Methods of measuring oxygenation levels of tissue that contains tumors is known in the art and described in, for example, Zhao, D., et al., Measuring changes in tumor oxygenation, Methods Enzymol. 2004; 386:378-418, doi.org/10.1016/S0076-6879(04)86018-X; and H Rundqvist and R S Johnson, Tumour oxygenation: implications for breast cancer prognosis, Intern Med 2013; 274: 105-112, doi: 10.1111/joim.12091, the contents of each of which are incorporated herein by reference. In some embodiments, tumor oxygenation may be measured by electron paramagnetic resonance imaging (EPR). EPR is known in the art and described in, for example, Abramovid Z., et al., (eds) 11th Mediterranean Conference on Medical and Biomedical Engineering and Computing 2007. IFMBE Proceedings, vol 16. Springer, Berlin, Heidelberg, doi.org/10.1007/978-3-540-73044-6_116, ISBN 978-3-540-73043-9; and Matsumoto, et al., Low-field paramagnetic resonance imaging of tumor oxygenation and glycolytic activity in mice, J. Clin. Invest. 118:1965-1973 (2008) doi:10.1172/JCI34928, the contents of each of which are incorporated herein by reference.

A Device to Rapidly Assess Metabolite Levels

The invention also includes a device or assay to rapidly measure levels of a metabolite of interest, for e.g., DHO. Plasma from a patient is run on the assay with the objective to determine the level of metabolite in the plasma. In the described assay, set levels of the target enzyme are added with known activity. The assay quantifies the amount of metabolite present in plasma by colorimetric changes, a competitive assay, or other techniques known in the field. In one embodiment, the objective is to quantify the amount of DHO after a dose of brequinar. A patient plasma specimen is collected. The plasma is run on the assay containing set amount of DHODH. Patient DHO may compete with colored DHO in the assay and cause a change in color that can be read out as a measure of DHO level in the plasma. In another embodiment, substrate and DHODH could be lyophilized in a blood collection tube. Blood drawn into the tube could provide a visible change in color to determine if DHO is below, at or above a specified threshold. This would enable point of care monitoring of metabolite levels for rapid adjustments in dose as needed.

Devices for Notification

The invention also includes devices for notifying a subject concerning a dosing regimen, such as a dosage of a therapeutic agent, timing for administration of a dose, timing for collection of a metabolite to determine dose adjustments, or any combination thereof, or an adjustment to a dosing regimen. The devices include a processor coupled to a memory unit. The memory unit drives the processor to receive data about a dose of a therapeutic agent, collect data from laboratory or point of care analysis of the metabolite tested, generate a notification about a dosing regimen or a change to the dosing regimen, and output the reminder to the subject.

The data received by the processor may contain any information related to a dose of an agent provided to a subject. For example, the data may include information about the agent, such as the name of the agent, a classification the agent, the dose or amount of the agent provided to the subject, the concentration, the formulation, and the like. The data may include the route of administration, such as oral or intravenous administration. The data may include the when the dose was administered to the subject, including the day, date, hour, minute, second, time zone, or any other temporal component. The data may include information concerning multiple doses of the agent that were administered to the subject. The data may include information concerning multiple agents that were administered to the subject. The data may include a metabolite level and whether a specified threshold has been reached.

The notification may include any type of reminder to the subject concerning the dosing regimen or adjustments thereto. For example, the notification may include a time for administration of the next dose of the agent, the dosage of the next dose of the agent, or a combination of the two. The notification may include adjustments to any of the aforementioned parameters. The notification may include information provided in absolute terms or relative terms. For example, the notification may include a time component that indicate that the next dose should be provided at a certain number of hours, e.g., 72 hours, following the previous dose, or it may indicate an objective time and/or date for administration of the next dose. The notification may indicate that the dosage should be adjusted by a defined amount, e.g., increased by 75 ng/mL, by a relative amount, e.g., increased by 50%. The dosing regimen or adjustment to the dosing regimen is based on a measured level of a metabolite in a sample obtained from the subject, as described above. The notification may also recommend the time for an additional blood collection for metabolite analysis based on a trend analysis of historic drug and metabolite levels, a change in disease, or new evidence for an alternative blood sampling schedule.

The device may provide the notification in any manner that can be perceived by the subject. For example, output of the notification may include an audible signal, a visual signal, a tactile signal, a vibration, or any combination thereof.

The device may output the notification to a component of the device, such as a display, or it may output the notification to a remote device. The device may output the notification to a third party, such as health care professional, e.g., a physician, nurse, or other practitioner.

The memory unit may enable the processor to perform additional processes. For example, the processor may determine a dosing regimen or an adjustment to a dosing regimen, as described above.

The processor may use information stored in the memory unit to determine whether the subject has developed or is developing resistance to a therapeutic agent. Resistance of a subject to a therapeutic agent can become manifest when the interval between time points of dose administration to achieve the same effect, e.g., level of metabolite, become smaller over the course of therapy, i.e., when the subject requires more frequent doses. Resistance of a subject to a therapeutic agent can become manifest when higher dosages are required to achieve the same effect, e.g., level of metabolite, over the course of therapy. Thus, the processor may determine that intervals between time points for administration of the agent have changed, e.g., grown smaller or larger, over the course of therapy, that dosages have changed, e.g., increased or decreased, over the course of therapy, or a combination of the two.

The processor may output a recommended adjustment in the dosing regimen to the subject. The recommended adjustment may include administration of a second or additional therapeutic agent.

The device may be, or be a part of, a portable or wearable electronic device, such as a phone, watch, belt, armband, legband, article of clothing, handheld device, or the like.

Synthetic Lethality

Methods of the invention include determining a dosing regimen that includes providing an agent that alters activity of a metabolic pathway in a tumor that is specifically dependent on that metabolic pathway. For example, tumor cells bearing a mutation that affects the activity of a first pathway may rely more heavily on the activity of a second pathway that compensates for or counteracts the altered activity of the first pathway. A change in the activity of the second pathway that may therefore be deadly to tumor cells but not to normal cells, a phenomenon called synthetic lethality. Examples of tumors with altered pathways for which a DHODH inhibitor, such as brequinar, may be synthetically lethal include tumors that have phosphatase and tensin homolog (PTEN) low, Myc protein family member amplification, a Notch protein family member mutations, and activating mutations of Ras protein family members.

Combination Therapies for Autoimmune Toxicity

Methods of the invention include determining a dosing regimen that includes providing an agent that alters activity of a metabolic pathway, as described above, in combination with one or more other therapeutic agents. The methods may also include providing both therapeutic agents in such combination dosing regimens.

Combination therapies are useful, for example, for treating autoimmune toxicity and cytokine-associated toxicity. Autoimmune toxicity may result from an antigen-specific attack on host tissues when the targeted tumor associated antigen is expressed on nonmalignant tissue. It may result due to increased immune activation due to immunoncology (IO) therapy. It may preferentially affect patients with pre-existing autoimmune disease such as rheumatoid arthritis, inflammatory bowel disease, and psoriasis.

Cytokine Release Syndrome (CRS)

Cytokine associated toxicity, also referred to as cytokine release syndrome (CRS) or cytokine storm, is a non-antigen specific toxicity that occurs as a result of high level immune activation. The degree of immune activation necessary to obtain clinical benefit using IO typically exceeds the level of immune activation that occurs during natural immune activation. As IO therapies have increased in potency and efficacy, CRS is increasingly recognized as a problem requiring a solution.

CRS is clinically observed in cases where large numbers of lymphocytes (B cells, T cells, and/or natural killer cells) and/or myeloid cells (macrophages, dendritic cells, and monocytes) become activated and release inflammatory cytokines including IL-1beta, TNFalpha, IFNbeta, IFNgamma, IL-6, and IL-8. CRS is caused by a hyperactivated T-cell response which is not tissue specific and thus causes reactivity with normal issue. This results in the production of high levels of CD4 T-helper cell cytokines or increased migration of cytolytic CD8 T cells within normal tissues. Weber, J. S., et al., “Toxicities of Immunotherapy for the Practitioner,” Journal of Clinical Oncology, 33, no. 18 (June 2015) 2092-2099. The onset of symptoms may occur within a period of minutes to hours after administration of an IO therapy. Timing of symptom onset and CRS severity may depend on the inducing agent and the magnitude of the resulting immune cell activation. CRS can lead to serious organ damage and failure; such injury includes pulmonary infiltrates, lung injury, acute respiratory distress syndrome, cardiac dysfunction, cardiovascular shock, neurologic toxicity, disseminated intravascular coagulation (DIC), hepatic failure, or renal failure.

CRS has been reported following the administration of IO therapies including HSCT, cancer vaccines (either alone or in combination with adoptive T-cell therapy), mAbs, and CAR-T cells. CRS is a potentially life-threatening toxicity, with some patients requiring extensive intervention and life support. Patients have experienced neurological damage and/or death. Diagnosis and management of CRS in response to immune cell-based therapies is routinely based on clinical parameters and symptoms. Lee et al. has described a revised CRS grading system, shown below in Table 3. Lee, D. et al. (2014) Blood 124(2): 188-195.

TABLE 3 Grade Toxicity Grade 1 Symptoms are not life threatening and require symptomatic treatment only, e.g., fever, nausea, fatigue, headache, myalgias, malaise Grade 2 Symptoms require and respond to moderate intervention Oxygen requirement <40% or Hypotension responsive to fluids or low dose of one vasopressor or Grade 2 organ toxicity Grade 3 Symptoms require and respond to aggressive intervention Oxygen requirement ≥40% or Hypotension requiring high dose or multiple vasopressors or Grade 3 organ toxicity or grade 4 transaminitis Grade 4 Life-threatening symptoms Requirement for ventilator support or Grade 4 organ toxicity (excluding transaminitis) Grade 5 Death Grades 2-4 refer to CTCA.E v4.0 grading

Standard treatment involves vigilant supportive care and treatment with immunosuppressive drugs (e.g., anti-cytokine antibodies such as tocilizumab and corticosteroids). Management of CRS must be balanced with ensuring the efficacy of IO treatments. While early and/or aggressive immunosuppression may mitigate CRS, it may also limit the efficacy of the therapy. There have been reports that CRS may actually be necessary for effective treatment. The goal of CRS management is not to completely suppress it, but to prevent life-threatening toxicity while maximizing any antitumor effects. Lee, D. et al. (2014) Blood 124(2): 188-195.

Immuno-Oncology Therapy

The present disclosure relates particularly to methods of improving the safety of immuno-oncology (IO) treatments while maintaining efficacy. Cancer or autoimmune disease may be viewed as the result of a dysfunction of the normal immune system. The goal of IO is to utilize a patient's own immune system to effect treatment of a disorder. IO treatments may include hematopoietic stem cell transplantation (HSCT), cancer vaccines, monoclonal antibodies (mAbs), and adoptive T-cell immunotherapy

Examples of Combination Therapies

Examples of therapeutic agents that can be used in combination dosing regimens are described below.

Agents that Target Metabolic Pathways

The second or additional therapeutic agent may target a metabolic pathway different from the pathway targeted by the primary therapeutic agent. For example, the second agent may inhibit a glutaminase, the PI3K pathway, or orotidine 5′-monophosphate (OMP) decarboxylase.

Other Anti-Cancer Agents

The second or additional therapeutic agent may be an anti-cancer agent used to treat brain cancer. For example and without limitation, the second agent may be carboplatin, carmustine, cisplatin, cyclophosphamide, etoposide, irinotecan, lomustine, methotrexate, procarbazine, temozolomide, or vincristine.

CAR T-Cell Therapy

Adoptive T-cell immunotherapy may be performed with either natural T-cells or with engineered T-cells. Engineered T-cells can include T-cells which have been engineered to express chimeric antigen receptors (CARs) on their surface (CAR-T cells).

Autologous adoptive cell transfer involves the collection, modification, and return of a patient's immune cells, offering a promising immunotherapeutic approach for the treatment of different types of cancers. Typically, leukocytes are isolated, usually by well established density barrier centrifugation, and T lymphocytes are expanded ex vivo using cell culture methods, often relying on the immunomodulatory action of interleukin-2. Once expanded, the cells are administered intravenously to the patent in an activated state. Such cells are referred to as effector T cells. In addition, a combination of anti-CD3 and anti-CD28 antibodies may be used as a surrogate for antigen presentation with appropriate co, stimulation cues to promote the proliferation of T cells in culture.

For T cells, engagement of the CD4⁺ and CD8⁺ T cell receptor (TCR) alone is not sufficient to induce persistent activation of resting naive or memory T cells. Fully functional, productive T cell activation requires a second co-stimulatory signal from a competent antigen-presenting cell (APC).

Co-stimulation is achieved naturally by the interaction of CD28, a co-stimulatory cell surface receptor on T cells, with a counter-receptor on the surface of the APC, e.g., CD80 and/or CD86. An APC may also be used for the antigen-dependent activation of T cells. To induce functional activation rather than toleragenic T cells, APCs must also express on their surface a co-stimulatory molecule. Such APCs are capable of stimulating T cell proliferation, inducing cytokine production, and acting as targets for cytolytic T lymphocytes (CTL) upon direct interaction with the T cell.

Recently, T cells have been genetically engineered to produce artificial T cell receptors on their surface called chimeric antigen receptors (CARs). CARs allow T cells to recognize a specific, pre-selected protein, or antigen, found on targeted tumor cells. CAR-T cells can be cultured and expanded in the laboratory, then re-infused to patients in a similar manner to that described above for adoptive transfer of native T cells. The CAR directs the CAR T-cell to a target cell expressing an antigen to which the CAR is specific. The CAR T cell binds the target and through operation of a stimulatory domain activates the CAR T-cell. In some embodiments, the stimulatory domain is selected from CD28, OX40, CD27, CD2, CD5, ICAM-1, LFA-1 (CD11a/CD18), 4-1BB, or a combination thereof.

CARs may be specific for any tumor antigen. In some embodiments, a CAR comprises an extracellular binding domain specific for a tumor antigen. In some embodiments, a tumor antigen is selected from TSHR, CD19, CD123, CD22, CD30, CD171, CS-1, CLL-1, CD33, EGFRvIII, GD2, GD3, BCMA, Tn Ag, PSMA, ROR1, FLT3, FAP, TAG72, CD38, CD44v6, CEA, EPCAM, B7H3, KIT, IL-13Ra2, Mesothelin, IL-llRa, PSCA, PRSS21, VEGFR2, LewisY, CD24, PDGFR-beta, SSEA-4, CD20, Folate receptor alpha, ERBB2 (Her2/neu), MUC1, EGFR, NCAM, Prostase, PAP, ELF2M, Ephrin B2, IGFI receptor, CAIX, LMP2, gplOO, bcr-abl, tyrosinase, EphA2, Fucosyl GM1, sLe, GM3, TGS5, HMWMAA, o-acetyl-GD2, Folate receptor beta, TEM1/CD248, TEM7R, CLDN6, GPRC5D, CXORF61, CD97, CD179a, ALK, Polysialic acid, PLAC1, GloboH, NY-BR-1, UPK2, HAVCR1, ADRB3, PANX3, GPR20, LY6K, OR51E2, TARP, WTi, NY-ESO-1, LAGE-la, MAGE-A1, legumain, HPV E6,E7, MAGE Al, ETV6-AML, sperm protein 17, XAGE1, Tie 2, MAD-CT-1, MAD-CT-2, Fos-related antigen 1, p53, p53 mutant, prostein, survivin and telomerase, PCTA-1/Galectin 8, MelanA/MARTI, Ras mutant, hTERT, sarcoma translocation breakpoints, ML-IAP, ERG (TMPRSS2 ETS fusion gene), NA17, PAX3, Androgen receptor, Cyclin Bi, MYCN, RhoC, TRP-2, CYP1B1, BORIS, SART3, PAX5, OY-TES1, LCK, AKAP-4, SSX2, RAGE-1, human telomerase reverse transcriptase, RU1, RU2, intestinal carboxyl esterase, mut hsp70-2, CD79a, CD79b, CD72, LAIR1, FCAR, LILRA2, CD300LF, CLEC12A, BST2, EMR2, LY75, GPC3, FCRL5, and IGLL1.

In some embodiments, a CAR comprises an extracellular binding domain specific for a tumor targeting antibody. In some embodiments, an extracellular binding domain specific for a tumor targeting antibody binds an Fc portion of a tumor targeting antibody. In some embodiments, an extracellular binding domain specific for a tumor targeting antibody comprises an Fc receptor or an Fc binding portion thereof. In some embodiments, an Fc receptor is an Fc-gamma receptor, an Fc-alpha receptor, or an Fc epsilon receptor. In some embodiments, an extracellular binding domain can be an extracellular ligand-binding domain of CD16 (e g., CD16A or CD16B), CD32 (e g., CD32A, or CD32B), or CD64 (e g., CD64A, CD64B, or CD64C).

In some embodiments, a CAR comprises a transmembrane domain. In some embodiments, a transmembrane domain is selected from CD8α, CD8β, 4-1BB, CD28, CD34, CD4, FcεRIγ, CD16 (e g., CD16A or CD16B), OX40, CD3ζ CD3ε, CD3γ, CD3δ, TCRα, CD32 (e g., CD32A or CD32B), CD64 (e g., CD64A, CD64B, or CD64C), VEGFR2, FAS, and FGFR2B, or a combination thereof. In some embodiments, the transmembrane domain is not CD8α. In some embodiments, a transmembrane domain is a non-naturally occurring hydrophobic protein segment.

In some embodiments, a CAR comprises a co-stimulatory domain for T-cell activation. In some embodiments, a co-stimulatory domain is selected from CD28, OX40, CD27, CD2, CD5, ICAM-1, LFA-1 (CD11a/CD18), 4-1BB, GITR, HVEM, TIM1, LFA1, or CD2, a functional fragment thereof, or a combination thereof. In some embodiments, a CAR comprises two or more co-stimulatory domains. In some embodiments, the two or more co-stimulatory domains are selected from CD28, OX40, CD27, CD2, CD5, ICAM-1, LFA-1 (CD11a/CD18), 4-1BB, GITR, HVEM, TIM1, LFA1, or CD2.

Cytokine release syndrome (CRS) is a common and potentially lethal complication of CAR-T cell therapy. It is a non-antigen specific toxicity that can occur as a result of the high-levels of CAR-T cell expansion and immune activation typically required to mediate clinical benefit using modem immunotherapies such as CAR-T cell transfer. Timing of symptom onset and CRS severity depends on the inducing agent and the magnitude of immune cell activation. Symptom onset typically occurs days to occasionally weeks after T cell infusion, coinciding with maximal in vivo T-cell expansion.

The incidence and severity of CRS following CAR-T therapy for cancer has recently been reported to be greater in patients having large tumor burdens. Without wishing to be bound by any theory, it is believe that this is due to the expression of production of pro-inflammatory cytokines such as TNF-α by the adoptively transferred expanding and activated CAR-T cell populations. CRS following CAR-T therapy has been consistently associated with elevated IFNγ, IL-6, and TNF-α levels, and increases in IL-2, granulocyte macrophage-colony-stimulating factor (GM-CSF), IL-10, IL-8, IL-5, and fracktalkine have also been reported.

Cancer Vaccines

In some embodiments an immune-oncology therapy is a cancer vaccine. A cancer vaccine is an immunogenic composition which stimulates a patient's immune system to produce anti¬tumor antibodies, thereby enabling the immune system to target and destroy cancerous cells. In some embodiments, a cancer vaccine is a peptide vaccine. In some embodiments, a cancer vaccine is a conjugate vaccine.

In some embodiments, a cancer vaccine is used in combination with adoptive T cell therapy. In some embodiments, a cancer vaccine is administered to a patient, after which tumor specific T cells are obtained from the patient, isolated, expanded ex vivo, and then administered to the patient. In some embodiments, the ex vivo expansion of tumor specific T cells provides for a method of obtaining a greater number of T cells which may attack and kill cancerous cells than what could be obtained by vaccination alone. In some embodiments, adoptive T cell therapy comprises culturing tumor infiltrating lymphocytes. In some embodiments, one particular T cell or clone is isolated and expanded ex vivo prior to administration to a patient. In some embodiments, a T cell is obtained from a patient who has received a cancer vaccine.

Administration of cancer vaccines, either alone or in combination with adoptive T cell transfer has been reported to result in CRS.

Human Stem Cell Transplantation (HSCT)

HSCT is the transplantation of stem cells to reestablish hematopoietic function in a patient with defective bone marrow or immune system. In some embodiments, the stem cells are autologous. In some embodiments, the stem cells are allogeneic. In some embodiments the transplant is performed by intravenous infusion.

In some embodiments, autologous HSCT may be used to treat multiple myeloma, non-Hodgkin lymphoma, Hodgkin disease, acute myeloid leukemia, neuroblastoma, germ cell tumors, autoimmune disorders (e.g., systemic lupus erythematosus [SLE], systemic sclerosis), or amyloidosis.

In some embodiments, allogeneic HSCT may be used to treat acute myeloid leukemia, acute lymphoblastic leukemia, chronic myeloid leukemia, chronic lymphocytic leukemia, myeloproliferative disorders, myelodysplastic syndromes, multiple myeloma, non-Hodgkin lymphoma, Hodgkin disease, aplastic anemia, pure red-cell aplasia, paroxysmal nocturnal hemoglobinuria, Fanconi anemia, thalassemia major, sickle cell anemia, severe combined immunodeficiency (SCID), Wiskott-Aldrich syndrome, hemophagocytic lymphohistiocytosis, inborn errors of metabolism, Epidermolysis Bullosa, severe congenital neutropenia, Shwachman-Diamond syndrome, Diamond-Blackfan anemia, or leukocyte adhesion deficiency.

In some embodiments, stem cells are obtained from a donor for administration to a patient. In some embodiments, the donor is an identical twin of the patient. In some embodiments, the donor is a matched donor related to the patient. In some embodiments, the donor is a matched donor unrelated to the patient. In some embodiments, the donor is a mismatched donor related to the patient. In some embodiments, the donor is haploidentical to the patient.

In some embodiments stem cells are obtained from bone marrow, peripheral blood, or umbilical cord blood.

HSCT may result in graft vs. host disease (GvHD), which remains a major cause of morbidity and mortality in patients undergoing HSCT. Even though there have been advances in prevention and post-transplant immunosuppressive strategies, it is estimated that 20-50% of all HSCT patients will experience at least moderate GvHD. Inflammatory cytokine release, e.g., CRS, is likely the primary mediator of acute GvHD, and activation of T-cells is one step in this complex process. Ball, L. M. & Egeler, R. M., “Acute GvHD: pathogenesis and classification,” Bone Marrow Transplantation (2008) 41, S58-S64. Bouchlaka, M. N., “Immunotherapy following hematopoietic stem cell transplantation: potential for synergistic effects,” Immunotherapy. 2010 May; 2(3): 399-418.

Monoclonal Antibodies (mAbs)

Monoclonal antibodies are useful in the treatment of various cancers. mAb cancer treatments utilize natural immune system functions to attack cancerous cells. Administration of mAbs specific for tumor antigens can be useful in targeting the tumor cells for destruction by the immune system. In some cases mAbs can trigger lysis of cancer cells, block cancer cell growth/replication, prevent angiogenesis, act as checkpoint inhibitors, and in some cases act to bind a tumor antigen while also activating specific immune cells. In some embodiments, a monoclonal antibody is monospecific. In some embodiments, a monoclonal antibody is bispecific. In some embodiments, a monoclonal antibody is a checkpoint inhibitor. In some embodiments, a mAb may be used in combination with CAR-T therapy.

When activated by therapeutic monoclonal antibodies, T-cell surface receptors can cause CRS. In some embodiments, antibodies which may induce CRS include anti-CD3 antibodies, anti-CD20 antibodies, anti-CD28 antibodies, anti-CTLA-4 antibodies, anti-PD-1 antibodies, and anti-PD-L1 antibodies. In some embodiments, antibodies which may induce CRS include alemtuzumab, muromonab-CD3, rituximab, tosituzumab, CP-870,893, LO-CD2a/BTI-322, TGN1412, pembrolizumab, nivolumab, or ipilimumab.

Other Therapeutic Interventions

The methods of the invention may combine the use of an agent that alters the activity of a metabolic pathway, such as the agents described above, with another therapeutic approach, such as surgery or radiotherapy.

Inhibitors of Nucleotide Synthesis Pathways

Methods of the invention include providing to a subject an agent that inhibits a nucleotide synthesis pathway. The pathway may be a synthetic pathway for pyrimidine-based nucleotides or a synthetic pathway for purine-based nucleotides, and the agent may inhibit an enzyme in such a pathway.

Several of the enzymes in the pyridine synthesis pathway are targets of drugs or drug candidates. For example, aspartate carbamoyltransferase (also known as aspartate transcarbamoylase or ATCase), which catalyzes the conversion of carbamoyl phosphate to carbamoyl aspartate, is inhibited by PALA (N-phosphoacetyl-L-aspartate); dihydroorotate dehydrogenase (DHODH), which catalyzes conversion of dihydroorotate (DHO) to orotate, is inhibited by brequinar, leflunomide, and teriflunomide; and orotidine monophosphate decarboxylase (OMPD), which catalyzes conversion of orotidine monophosphate (OMP) to uridine monophosphate (UMP), is inhibited by pyrazofurin.

Several enzymes involved in purine biosynthesis are also of therapeutic interest. For example, inosine-5′-monophosphate dehydrogenase (IMPDH), which catalyzes conversion of inosine-5′-monophosphate (IMP) to xanthosine monophosphate (XMP), the first committed step in de novo synthesis of guanine nucleotides from IMP, is inhibited by tiazofurin; hypoxanthine/guanine phosphoribosyl transferase (HGPRT), which catalyzes conversion of hypoxanthine to inosine monophosphate and guanine to guanosine monophosphate in the purine salvage pathway, is inhibited by 6-mercaptopurine; and dihydrofolate reductase (DHFR), which reduces dihydrofolic acid to tetrahydrofolic acid in the purine salvage pathway, is inhibited by methotrexate.

Because many of the enzymes involved in pyrimidine or purine biosynthesis are the targets of known inhibitors, metabolites in these pathways can serve as indicators of engagement of therapeutic agents with their targets. For example, the utility of DHO as an indicator of target engagement by DHODH inhibitors has been described in for example, International Patent Publication Nos. WO 2019/191030 and WO 2019/191032, the contents of which are incorporated herein by reference. One advantage of DHO is that cell membranes are permeable to the molecule. DHODH is localized to the mitochondrial inner membrane within cells, making direct measurement of enzyme activity difficult. However, DHO, which accumulates when DHODH is inhibited, diffuses out of cells and into the blood, which can be easily sampled. DHO is also sufficiently stable that levels of the metabolite can be measured reliably. Thus, by analyzing levels of DHO in blood or blood products, one can readily assess target engagement of a DHODH inhibitor.

Several other metabolites can serve as indicators of target engagement for inhibitors of other enzymes involved in nucleotide synthesis in an analogous manner. For example and without limitation, inhibition of OMPD can be gauged by measurement of levels of orotate or OMP, and inhibition of IMPDH can be gauged by measurement of levels of IMP.

The same principles can be applied to inhibitors of other pathways as well. For example, many inhibitors of fatty acid amide hydrolase, an enzyme in the anandamide degradation pathway, are known, and some have been investigated as potential antineoplastic agents. Thus, metabolites in the anandamide degradation could serve as indicators for target engagement by such inhibitors. It will be understood by one of ordinary skill that assessing engagement of an agent that inhibits an enzyme by analyzing levels of a substrate or related compound is broadly applicable and not limited to the pathways described above.

Some agents that may be used in embodiments of the invention are described below.

Brequinar, 6-fluoro-2-(2′-fluoro-1,1′ biphenyl-4-yl)-3-methyl-4-quinoline carboxylic acid, has the following structure:

Brequinar and related compounds are described in, for example, U.S. Pat. Nos. 4,680,299 and 5,523,408, the contents of which are incorporated herein by reference. The use of brequinar to treat leukemia is described in, for example, U.S. Pat. No. 5,032,597 and International Publication No. WO 2017/037022, the contents of which are incorporated herein by reference.

Leflunomide, N-(4′-trifluoromethylphenyl)-5-methylisoxazole-4-carboxamide (I), is described in, for example, U.S. Pat. No. 4,284,786, the contents of which are incorporated herein by reference.

Teriflunomide, 2-cyano-3-hydroxy-N-[4-(trifluoromethyl)phenyl]-2-butenamide, is described in, for example, U.S. Pat. No. 5,679,709, the contents of which are incorporated herein by reference.

Pyrazofurin, 5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1H-pyrazole-3-carboxamide, has the following structure:

Pyrazofurin and related compounds are described in, for example, U.S. Pat. Nos. 3,674,774 and 3,802,999, the contents of which are incorporated herein by reference.

N-(phosphonacetyl)-L-aspartate (PALA) is described in, for example, Swyryd et al, N-(Phosphonacetyl)-L-Aspartate, a Potent Transition State Analog Inhibitor of Aspartate Transcarbamylase, Blocks Proliferation of Mammalian Cells in Culture, J. Biol. Chem. Vol. 249, No. 21, Issue of November 10, pp. 6945-6950, 1974, the contents of which are incorporated herein by reference.

Tiazofurin, 2-β-D-ribofuranosylthiazole-4-carboxamide, has the following structure:

Tiazofurin and methods for making it are known in the art and described in, for example, U.S. Pat. Nos. 4,451,648 and 6,613,896, the contents of which are incorporated herein by reference. Tiazofurin analogs, their activity against tumors, and methods of making them are described in, for example, Popsavin, et al., Synthesis and antiproliferative activity of two new tiazofurin analogues with 2′-amido functionalities, Bioorg. Med. Chem. Lett. 16 (2006) 2773-2776, doi: 10.1016/j.bmcl.2006.02.001; and Popsavin, et al., Synthesis and in vitro antitumour activity of tiazofurin analogues with nitrogen functionalities at the C-2′ position, European Journal of Medicinal Chemistry 111 (2016) 114e125. doi: 10.1016/j.ejmech.2016.01.037, the contents of each of which are incorporated herein by reference.

Many other inhibitors of IMPDH are known in the art. For example and without limitation, other IMPDH inhibitors include AS2643361, EICAR, FF-10501, mizoribine, mycophenolic acid, ribavirin, selenazofurin, SM-108, taribavirin, VX-148, VX-497, and VX-944. Other IMPDH inhibitors are described in Gebeyehu, G., et al., Ribavirin, Tiazofurin, and Selenazofurin: Mononucleotides and Nicotinamide Adenine Dinucleotide Analogues. Synthesis, Structure, and Interactions with IMP Dehydrogenase, J. Med. Chem. 1985, 28, 99-105; and U.S. Pat. Nos. 5,807,876; 6,344,465; 6,395,763; 6,399,773; 6,420,403; 6,518,291; 6,541,496; 6,617,323; 6,624,184; 6,653,309; 6,825,224; 6,867,299; 6,919,335; 6,967,214; 7,053,111; 7,060,720; 7,087,642; 7,205,324; 7,329,681; 7,432,290; 7,777,069; and 7,989,498, the contents of each of which are incorporated herein by reference.

In methods that involve administration of brequinar to a subject, brequinar may be provided as a brequinar analog, a brequinar derivative, a brequinar prodrug, a micellar formulation of brequinar, a brequinar hydrate, or a brequinar salt. The brequinar salt may be a sodium salt.

Providing an Agent to a Subject

Any of the agents described above may be provided to a subject by any suitable route of administration. For example and without limitation, the agent may be provided orally, intravenously, enterally, parenterally, dermally, buccally, topically, transdermally, by injection, subcutaneously, nasally, pulmonarily, or with or on an implantable medical device.

The agent may be provided to a subject following exposure or suspected exposure to a virus to prevent or treat a viral infection. For example, the agent may be provided to a subject that has come into contact with, or proximity to, one or more individuals who are infected with a virus or are suspected of being infected with a virus. The agent may be provided at a defined period following exposure or suspected exposure to the virus. For example and without limitation, the agent may be provided about 5 minutes, about 10 minutes, about 15 minutes, about 30 minutes, about 1 hour, about 2 hours, about 3 hours, about 4 hours, about 6 hours, about 8 hours, about 12 hours, about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, or about 7 days after exposure or suspected exposure to the virus.

Alternatively or additionally, the agent may be provided to a subject prophylactically to prevent or minimize the severity of a viral infection. For example, the agent may be provided to a subject that is about to come into contact with, or proximity to, one or more individuals who are infected with a virus or are suspected of being infected with a virus. The agent may be provided at a defined period prior to exposure or suspected exposure to the virus. For example and without limitation, the agent may be provided about 5 minutes, about 10 minutes, about 15 minutes, about 30 minutes, about 1 hour, about 2 hours, about 3 hours, about 4 hours, about 6 hours, about 8 hours, about 12 hours, about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, or about 7 days prior to exposure or suspected exposure to the virus.

The agents, including prodrugs, analogs, derivatives, and salts thereof, may be provided as pharmaceutical compositions. A pharmaceutical composition may be in a form suitable for oral use, for example, as tablets, troches, lozenges, fast-melts, aqueous or oily suspensions, dispersible powders or granules, emulsions, hard or soft capsules, syrups, or elixirs. Compositions intended for oral use may be prepared according to any method known in the art for the manufacture of pharmaceutical compositions and such compositions may contain one or more agents selected from sweetening agents, flavoring agents, coloring agents and preserving agents, in order to provide pharmaceutically elegant and palatable preparations. Tablets contain the compounds in admixture with non-toxic pharmaceutically acceptable excipients which are suitable for the manufacture of tablets. These excipients may be, for example, inert diluents, such as calcium carbonate, sodium carbonate, lactose, calcium phosphate or sodium phosphate; granulating and disintegrating agents, for example corn starch, or alginic acid; binding agents, for example starch, gelatin or acacia, and lubricating agents, for example magnesium stearate, stearic acid or talc.

The tablets may be uncoated, or they may be coated by known techniques to delay disintegration in the stomach and absorption lower down in the gastrointestinal tract and thereby provide a sustained action over a longer period. For example, a time delay material such as glyceryl monostearate or glyceryl distearate may be employed. They may also be coated by the techniques described in U.S. Pat. Nos. 4,256,108, 4,166,452 and 4,265,874, to form osmotic therapeutic tablets for control release. Preparation and administration of compounds is discussed in U.S. Pat. No. 6,214,841 and U.S. Pub. No. 2003/0232877, the contents of each of which are incorporated by reference herein.

Formulations for oral use may also be presented as hard gelatin capsules in which the compounds are mixed with an inert solid diluent, for example calcium carbonate, calcium phosphate or kaolin, or as soft gelatin capsules in which the compounds are mixed with water or an oil medium, for example peanut oil, liquid paraffin or olive oil. An alternative oral formulation, where control of gastrointestinal tract hydrolysis of the compound is sought, can be achieved using a controlled-release formulation, where a compound of the invention is encapsulated in an enteric coating.

Aqueous suspensions may contain the compounds in admixture with excipients suitable for the manufacture of aqueous suspensions. Such excipients are suspending agents, for example sodium carboxymethylcellulose, methylcellulose, hydroxypropylmethylcellulose, sodium alginate, polyvinylpyrrolidone, gum tragacanth and gum acacia; dispersing or wetting agents such as a naturally occurring phosphatide, for example lecithin, or condensation products of an alkylene oxide with fatty acids, for example, polyoxyethylene stearate, or condensation products of ethylene oxide with long chain aliphatic alcohols, for example heptadecaethyleneoxycetanol, or condensation products of ethylene oxide with partial esters derived from fatty acids and a hexitol such a polyoxyethylene with partial esters derived from fatty acids and hexitol anhydrides, for example polyoxyethylene sorbitan monooleate. The aqueous suspensions may also contain one or more preservatives, for example ethyl, or n-propyl p-hydroxybenzoate, one or more coloring agents, one or more flavoring agents, and one or more sweetening agents, such as sucrose or saccharin.

Oily suspensions may be formulated by suspending the compounds in a vegetable oil, for example, arachis oil, olive oil, sesame oil or coconut oil, or in a mineral oil such as liquid paraffin. The oily suspensions may contain a thickening agent, for example beeswax, hard paraffin or cetyl alcohol. Sweetening agents such as those set forth above, and flavoring agents may be added to provide a palatable oral preparation. These compositions may be preserved by the addition of an antioxidant such as ascorbic acid.

Dispersible powders and granules suitable for preparation of an aqueous suspension by the addition of water provide the compounds in admixture with a dispersing or wetting agent, suspending agent and one or more preservatives. Suitable dispersing or wetting agents and suspending agents are exemplified, for example sweetening, flavoring, and coloring agents, may also be present.

The pharmaceutical compositions may also be in the form of oil-in-water emulsions. The oily phase may be a vegetable oil, for example olive oil or arachis oil, or a mineral oil, for example liquid paraffin or mixtures of these. Suitable emulsifying agents may be naturally-occurring gums, for example gum acacia or gum tragacanth, naturally occurring phosphatides, for example soya bean, lecithin, and esters or partial esters derived from fatty acids and hexitol anhydrides, for example sorbitan monooleate and condensation products of the said partial esters with ethylene oxide, for example polyoxyethylene sorbitan monooleate. The emulsions may also contain sweetening and flavoring agents.

Syrups and elixirs may be formulated with sweetening agents, such as glycerol, propylene glycol, sorbitol or sucrose. Such formulations may also contain a demulcent, a preservative, and agents for flavoring and/or coloring.

The pharmaceutical compositions may be in the form of a sterile injectable aqueous or oleaginous suspension. This suspension may be formulated according to the known art using those suitable dispersing or wetting agents and suspending agents which have been mentioned above. The sterile injectable preparation may also be in a sterile injectable solution or suspension in a non-toxic parenterally acceptable diluent or solvent, for example as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution, and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose, any bland fixed oil may be employed including synthetic mono- or di-glycerides. In addition, fatty acids such as oleic acid find use in the preparation of injectables.

Pharmaceutical compositions may include other pharmaceutically acceptable carriers, such as sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients, such as cocoa butter and suppository waxes; oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; glycols, such as propylene glycol; polyols, such as glycerin (glycerol), erythritol, xylitol. sorbitol, mannitol and polyethylene glycol; esters, such asethyl oleate and ethyllaurate; agar; buffering agents, such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol; pH buffered solutions; polyesters, polycarbonates and/or polyanhydrides; and other non-toxic compatible substances employed in pharmaceutical formulations. The pharmaceutically acceptable carrier may be an encapsulation coating. For example, the encapsulation coating may contain carrageenan, cellulose acetate phthalate, cellulose acetate succinate, cellulose acetate trimellitate, collagen, gelatin, hydroxypropyl methyl cellulose acetate, a methyl acrylate-methacrylic acid copolymer, polyvinyl acetate phthalate shellac, sodium alginate, starch, or zein.

The agents, including prodrugs, analogs, derivatives, and salts thereof, may be provided as pharmaceutically acceptable salts, such as nontoxic acid addition salts, which are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange. In some embodiments, pharmaceutically acceptable salts include, but are not limited to, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphor sulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Other pharmaceutically acceptable salts may be found in, for example, Remington, The Science and Practice of Pharmacy (20th ed. 2000). Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. In some embodiments, a pharmaceutically acceptable salt is an alkali salt. In some embodiments, a pharmaceutically acceptable salt is a sodium salt. In some embodiments, a pharmaceutically acceptable salt is an alkaline earth metal salt. In some embodiments, pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counter ions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, alkyl having from 1 to 6 carbon atoms, sulfonate and aryl sulfonate.

Dosing Regimens

Methods of the invention include providing a nucleotide synthesis inhibitor, such as brequinar or a pharmaceutically acceptable salt thereof, to a subject according to a dosing regimen. A dosing regimen may include a dosage and a schedule of administration. A dosage of brequinar includes an amount of the drug. The amount of brequinar may be expressed in absolute terms, e.g., mass of brequinar. The amount of brequinar may be expressed in terms relating the amount to the subject, e.g., brequinar mass per subject mass, or brequinar mass per subject volume. The amount of brequinar may be expressed in terms that indicate an effect of the drug, e.g., amount of brequinar that achieves a target concentration in a tissue or sample from the subject. A dosage may include a period of time over which the amount is to be administered to the subject. Thus, the dosage may include an amount of brequinar per unit of time. The dosage may include a single dose, i.e., the entire amount may be provided at once. Alternatively, the dosage may include multiple, e.g., 2, 3, 4, 6, or 8, doses that collectively achieve the entire amount of the dosage. A schedule of administration may be described by the interval between doses, e.g., every 24 hours, every 48 hours, etc., or by the number doses administered during a given period, e.g., once per week, twice per week, etc.

For example and without limitation, in some methods of the invention, the dosage of brequinar may be from about 10 mg to about 180 mg, from about 26 mg to about 180 mg, from about 51 mg to about 180 mg, from about 76 mg to about 180 mg, from about 101 mg to about 180 mg, from about 126 mg to about 180 mg, from about 151 mg to about 180 mg, from about 10 mg to about 150 mg, from about 26 mg to about 150 mg, from about 51 mg to about 150 mg, from about 76 mg to about 150 mg, from about 101 mg to about 150 mg, from about 126 mg to about 150 mg, from about 10 mg to about 125 mg, from about 26 mg to about 125 mg, from about 51 mg to about 125 mg, from about 76 mg to about 125 mg, from about 101 mg to about 125 mg, from about 10 mg to about 100 mg, from about 26 mg to about 100 mg, from about 51 mg to about 100 mg, from about 76 mg to about 100 mg, from about 10 mg to about 75 mg, from about 26 mg to about 75 mg, from about 51 mg to about 75 mg, from about 10 mg to about 50 mg, from about 26 mg to about 50 mg, about 10 mg, about 25 mg, about 50 mg, about 75 mg, about 100 mg, about 125 mg, about 150 mg, or about 180 mg. In some methods of the invention, the dosage of brequinar may be from about 10 mg to about 4000 mg, from about 26 mg to about 4000 mg, from about 51 mg to about 4000 mg, from about 76 mg to about 4000 mg, from about 101 mg to about 4000 mg, from about 151 mg to about 4000 mg, from about 201 mg to about 4000 mg, from about 10 mg to about 2000 mg, from about 26 mg to about 2000 mg, from about 51 mg to about 2000 mg, from about 76 mg to about 2000 mg, from about 101 mg to about 2000 mg, from about 151 mg to about 2000 mg, from about 201 mg to about 2000 mg, from about 10 mg to about 1000 mg, from about 26 mg to about 1000 mg, from about 51 mg to about 1000 mg, from about 76 mg to about 1000 mg, from about 101 mg to about 1000 mg, from about 151 mg to about 1000 mg, from about 201 mg to about 1000 mg, from about 10 mg to about 500 mg, from about 26 mg to about 500 mg, from about 51 mg to about 500 mg, from about 76 mg to about 500 mg, from about 101 mg to about 500 mg, from about 151 mg to about 500 mg, from about 201 mg to about 500 mg, from about 10 mg to about 300 mg, from about 26 mg to about 300 mg, from about 51 mg to about 300 mg, from about 76 mg to about 300 mg, from about 101 mg to about 300 mg, from about 151 mg to about 300 mg, from about 201 mg to about 300 mg, from about 10 mg to about 200 mg, from about 26 mg to about 200 mg, from about 51 mg to about 200 mg, from about 76 mg to about 200 mg, from about 101 mg to about 200 mg, from about 151 mg to about 200 mg, from about 10 mg to about 150 mg, from about 26 mg to about 150 mg, from about 51 mg to about 150 mg, from about 76 mg to about 150 mg, from about 101 mg to about 150 mg, from about 10 mg to about 100 mg, from about 26 mg to about 100 mg, from about 51 mg to about 100 mg, from about 76 mg to about 100 mg, about 50 mg, about 75 mg, about 100 mg, about 200 mg, about 250 mg, about 300 mg, about 400 mg, about 500 mg, about 1000 mg, about 2000 mg, or about 4000 mg.

For example and without limitation, the dosage of brequinar may be an amount sufficient to maintain a concentration of brequinar in a lung of the subject of at least 0.01 μg/mL, at least 0.03 μg/mL, at least 0.1 μg/mL, at least 0.2 μg/mL, at least 0.3 μg/mL, at least 0.375 μg/mL, at least 0.4 μg/mL, at least 0.5 μg/mL, at least 0.6 μg/mL, at least 0.8 μg/mL, at least 1 μg/mL, at least 1.5 μg/mL, or at least 2 μg/mL for a 24-hour period.

A dosing regimen may contain a single dosage. Alternatively, a dosing regimen may contain multiple dosages. For example, a dosing regimen may include 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more dosages. A dosing regimen may include multiple dosages provided consecutively. For example, a dosage may include a defined amount of brequinar provided over a defined period, e.g., one day or 24 hours, and the dosing regimen may include dosages provided in two or more consecutive periods, e.g., days or 24-hour periods.

In dosing regimens that include multiple dosages, each dosage may be the same, i.e., each includes the same amount of brequinar. Alternatively, dosing regimens may include dosages that are not all the same. In some embodiments, the dosing regimen includes multiple consecutive dosages in which the first one, two, three, or four dosages are higher than subsequent dosages. In some embodiments, the dosing regimen includes multiple consecutive dosages in which the first the first one, two, three, or four dosages are lower than subsequent dosages. In the aforementioned embodiments, the subsequent dosages may all the same, or they may differ from each other as well. A variety of other dosage variations are possible within the scope of the invention. For example and without limitation, the dosing regimen may include any of the following sequences of dosages: alternation between high and low dosages; stepwise decreases or increases in individual dosages; stepwise decreases or increases in which one or more steps include two or more dosages that are the same; and patterns in which one or more of the aforementioned sequences is repeated or interspersed another aforementioned sequence. Each dosage may independently be selected from any of the dosages described above. For example, the first dosage may be 100 mg, and the subsequent dosages may be 25 mg, 50 mg, or 75 mg.

The dosing regimen may include a dosage-free period in which the subject does not receive brequinar or a pharmaceutically acceptable salt thereof. The dosage-free period may be at least 12 hours, at least 24 hours, at least 36 hours, at least 48 hours, at least 60 hours, at least 72 hours, at least 5 days, at least 7 days, at least 10 days, at least 14 days, about 12 hours, about 24 hours, about 36 hours, about 48 hours, about 60 hours, about 72 hours, about 5 days, about 7 days, about 10 days, or about 14 days.

The dosage-free period may follow a dosage. The dosage-free period may follow multiple dosages provided over consecutive 24-hour periods. The dosage-free period may follow multiple dosages provided over 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 consecutive 24-hour periods.

The methods may include administering brequinar or a pharmaceutically acceptable salt thereof to a subject at a dosage level at or near a level that inhibit viral replication. Such dosage may be supplemented with a later dose at a reduced level, or by discontinuing of dosing. For example, the method may include administering a plurality of doses of brequinar according to a regimen characterized by at least first and second phases, wherein the first phase involves administration of at least one bolus dose of brequinar at a level that inhibits replication, and the second phase involves either administration of at least one dose that is lower than the bolus dose or absence of administration of brequinar.

In some embodiments, brequinar or a pharmaceutically acceptable salt thereof is not administered during a second phase. In some embodiments, a second phase involves administration of uridine rescue therapy. In some embodiments, a bolus dose is or comprises a dose that inhibits viral replication.

In some embodiments, the first phase and the second phase each comprise administering brequinar or a pharmaceutically acceptable salt thereof. In some embodiments, the first phase and the second phase are at different times. In some embodiments, the first phase and the second phase are on different days. In some embodiments, the first phase lasts for a period of time that is less than four days. In some embodiments, the first phase comprises administering brequinar, followed by a period of time in which no brequinar is administered. In some embodiments, the period of time in which no brequinar is administered is 3 to 7 days after the dose during the first phase. In some embodiments, the first phase comprises administering more than one dose.

In some embodiments, brequinar or a pharmaceutically acceptable salt thereof is administered during a second phase. In some embodiments, brequinar is administered at levels that do not inhibit viral replication during the second phase. In some embodiments, the first phase is repeated after the second phase. In some embodiments, both the first and second phases are repeated.

In some embodiments, the present disclosure provides a method of administering brequinar or a pharmaceutically acceptable salt thereof to a subject in need thereof according to a multi-phase protocol comprising a first phase in which at least one dose of brequinar is administered to the subject and a second phase in which at least one dose of brequinar is administered to the subject, wherein one or more doses administered in the second phase differs in amount and/or timing relative to other doses in its phase as compared with the dose(s) administered in the first phase.

In some embodiments, the level of a metabolite, e.g. DHO, is determined in a sample from the subject between the first and second phases. In some embodiments, the sample is a plasma sample. In some embodiments, the timing or amount of at least one dose administered after the metabolite level is determined or differs from that of at least one dose administered before the metabolite level was determined.

In some embodiments, the amount of brequinar that is administered to the patient is adjusted in view of the metabolite level in the subject's plasma. For example, in some embodiments, a first dose is administered in the first phase. In some embodiments, metabolite level is determined at a period of time after administration of the first dose.

In some embodiments, if the metabolite level is below a pre-determined level, the amount of brequinar administered in a second or subsequent dose is increased and/or the interval between doses is reduced. For example, in some such embodiments, the amount of brequinar administered may be increased, for example, by 5 mg/m², 10 mg/m², 20 mg/m², 25 mg/m², 40 mg/m², 50 mg/m², 60 mg/m², 75 mg/m², or 100 mg/m². In some embodiments, the amount of brequinar administered in a second or subsequent dose is increased by 5 mg/m², 10 mg/m², 20 mg/m², 25 mg/m², 40 mg/m², 50 mg/m², 60 mg/m², 75 mg/m², 100 mg/m², 125 mg/m², 150 mg/m², 175 mg/m², or 200 mg/m². In some embodiments, the amount of brequinar administered may be increased by an adjustment amount determined based on change in metabolite levels observed between prior doses of different amounts administered to the subject. The dose may be increased by an absolute amount. For example and without limitation, the amount of brequinar administered may be increased by 5 mg, 10 mg, 20 mg, 25 mg, 40 mg, 50 mg, 60 mg, 75 mg, or 100 mg.

In some embodiments, if the metabolite level is above a pre-determined level, the amount of brequinar administered in a second or subsequent dose is the same as the amount administered in the first or previous dose and/or the interval between doses is the same.

In some embodiments, if the metabolite level is above a pre-determined level, the amount of brequinar in a second or subsequent dose is decreased and/or the interval between doses is increased. For example, in some such embodiments, the amount of brequinar administered may be decreased, for example, by 5 mg/m², 10 mg/m², 20 mg/m², 25 mg/m², 40 mg/m², 50 mg/m², 60 mg/m², 75 mg/m², or 100 mg/m². In some embodiments, if the metabolite level is above a pre-determined level, the amount of brequinar in a second or subsequent dose is decreased by 5 mg/m², 10 mg/m², 20 mg/m², 25 mg/m², 40 mg/m², 50 mg/m², 60 mg/m², 75 mg/m², 100 mg/m², 125 mg/m², 150 mg/m², 175 mg/m², or 200 mg/m². In some embodiments, the amount of brequinar administered may be decreased by an adjustment amount determined based on change in metabolite levels observed between prior doses of different amounts administered to the subject. The dose may be decreased by an absolute amount. For example and without limitation, the amount of brequinar administered may be decreased by 5 mg, 10 mg, 20 mg, 25 mg, 40 mg, 50 mg, 60 mg, 75 mg, or 100 mg.

In some embodiments, the present disclosure provides a method of administering a later dose of brequinar to a patient who has previously received an earlier dose of brequinar, wherein the patient has had a level of metabolite assessed subsequent to administration of the earlier dose, and wherein the later dose is different than the earlier dose. The later dose may be different from the earlier dose in amount of brequinar included in the dose, time interval relative to an immediately prior or immediately subsequent dose, or combinations thereof. The amount of brequinar in the later dose may be less than that in the earlier dose.

The method may include administering multiple doses of brequinar or a pharmaceutically acceptable salt thereof in which doses are separated from one another by a time period that is longer than 2 days and shorter than 8 days. For example, the time period may be about 3 days.

In some embodiments, the metabolite level is determined in a sample from the subject before each dose is administered, and dosing is delayed or skipped if the determined metabolite level is above a pre-determined threshold. For example, the metabolite level may be determined about 12 hours, about 24 hours, about 36 hours, about 48 hours, about 60 hours, about 72 hours, about 84 hours, or about 96 hours after administration of brequinar.

The method may include administering brequinar or a pharmaceutically acceptable salt thereof according to a regimen approved in a trial in which a level of metabolite was measured in a patient between doses of brequinar. The regimen may include multiple doses whose amount and timing were determined in the trial to maintain the metabolite level within a range determined to indicate a degree of target enzyme inhibition below a toxic threshold and above a minimum threshold. The regimen may include determining the metabolite level in the subject after administration of one or more doses of brequinar.

In some embodiments, the regimen includes a dosing cycle in which an established pattern of doses is administered over a first period of time. In some embodiments, the regimen comprises a plurality of the dosing cycles. In some embodiments, the regimen includes a rest period during which brequinar is not administered between the cycles.

Compositions that contain brequinar or a brequinar salt may contain a solid form of the drug. Compositions may contain crystals of brequinar or a brequinar salt, such as brequinar sodium. Crystals of brequinar sodium exist in at east least ten different polymorphic forms, labeled A-J. Compositions may contain a specific polymorphic form of brequinar sodium. For example, compositions may contain polymorphic form A, polymorphic form B, polymorphic form C, polymorphic form D, polymorphic form E, polymorphic form F, polymorphic form G, polymorphic form H, polymorphic form I, or polymorphic form J of brequinar sodium. Compositions may contain all or nearly all of the brequinar sodium salt in polymorphic form C. For example and without limitation, the composition may contain a brequinar sodium salt in which at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% of the brequinar sodium salt is polymorphic form C.

Viral Infections

Methods of the invention are useful for treating viral infections. In particular, the methods are useful for treating viral infections of the respiratory system. Respiratory viral infections include any viral infection of any tissue or cell type within the respiratory system. The infection may occur in the upper respiratory system, lower respiratory system, or both. For example and without limitation, the infection may occur in the alveoli, bronchi, bronchioles, larynx, lungs, nasal cavities, nose, pharynx, respiratory system, sinuses, or trachea.

The infection may include any type of virus that targets the respiratory system. For example and without limitation, the virus may be an adenovirus, coronavirus, human metapneumovirus, human parainfluenza virus, human respiratory syncytial virus, influenza virus, or rhinovirus. The coronavirus may be Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The influenza virus may be influenza A, influenza B, influenza C, or influenza D. The influenza A virus may be a H1N1, H3N2, N9N2, or H5N1 strain.

Combination Therapies

Methods of the invention may include providing brequinar or a pharmaceutically acceptable salt thereof to a subject in conjunction with one or more other agents. For example, the other agent may be a direct-acting antiviral agent, such as an agent that interferes with the function of a viral protein or enzyme. The other agent may be an anti-inflammatory agent.

For example and without limitation, the antiviral agent may be a 3C-like main protease inhibitor, eIF4E inhibitor, helicase inhibitor, inhibitor or a viral protein that binds to a host receptor, inhibitor of a viral structural protein, inhibitor of a virulence factor, inosine monophosphate dehydrogenase (IMPDH) inhibitor, interferon, papain-like proteinase inhibitor, protease inhibitor, RNA-dependent RNA polymerase inhibitor, or xanthine oxidase inhibitor.

The 3C-like main protease inhibitor may be (1S,2R,4aS,5R,8aS)-1-formamido-1,4a-dimethyl-6-methylene-5-((E)-2-(2-oxo-2,5-dihydrofuran-3-yl)ethenyl)decahydronaphthalen-2-yl 5-((R)-1,2-dithiolan-3-yl) pentanoate, (1S,2R,4aS,5R,8aS)-1-formamido-1,4a-dimethyl-6-methylene-5-((E)-2-(2-oxo-2,5-dihydrofuran-3-yl)ethenyl)decahydronaphthalen-2-yl 2-nitrobenzoate, (S)-(1S,2R,4aS,5R,8aS)-1-formamido-1,4a-dimethyl-6-methylene-5-((E)-2-(2-oxo-2,5-dihydrofuran-3-yl)ethenyl)decahydronaphthalen-2-yl-2-amino-3-phenylpropanoate, 2-((1R,5R,6R,8aS)-6-Hydroxy-5-(hydroxymethyl)-5,8a-dimethyl-2-methylenedecahydronaphthalen-1-yl)ethyl benzoate, 20-Hydroxy-3, 4-seco-friedelolactone-27-oic acid, alfuzosin, almitrine, amprenavir, andrograpanin, andrographiside, betulonal, carminic acid, carvedilol, cefpiramide, cerevisterol, chlorhexidine, chrysin-7-O-β-glucuronide, cilastatin, cosmosiin, demeclocycline, famotidine, flavin mononucleotide, hesperidin, isodecortinol, lutein, lymecycline, mimosine, montelukast, neohesperidin, nepafenac, phenethicillin, progabide, or tigecycline.

The eIF4E inhibitor may be ribavirin.

The IMPDH inhibitor may be AS2643361, EICAR, FF-10501, mizoribine, mycophenolic acid, mycophenolate mofetil, ribavirin, selenazofurin, SM-108, taribavirin, tiazofurin, VX-148, VX-497, or VX-944.

The interferon may be peginterferon alpha-2a or peginterferon alpha-2b.

The papain-like proteinase inhibitor may be (−)-epigallocatechin gallate, (S)-(1S,2R,4aS,5R,8aS)-1-formamido-1,4a-dimethyl-6-methylene-5-((E)-2-(2-oxo-2,5-dihydrofuran-3-yl)ethenyl) decahydronaphthalen-2-yl-2-amino-3-phenylpropanoate, 2-(3,4-dihydroxyphenyl)-2-[[2-(3,4-dihydroxyphenyl)-3,4-dihydro-5,7-dihydroxy-2H-1-benzopyran-3-yl]oxy]-3,4-dihydro-2H-1-benzopyran-3,4,5,7-tetrol, 2,20-cyclocytidine, 2,2-di (3-indolyl)-3-indolone, acetophenazine, ademetionine, aspartame, baicalin, cefamandole, chloramphenicol, chlorphenesin carbamate, chrysin, dantrolene, doxycycline, floxuridine, glutathione, hesperetin, iopromide, isotretinoin, L(+)-ascorbic acid, levodropropizine, magnolol, masoprocol, neohesperidin, nicardipine, oxprenolol, pemetrexed, phaitanthrin D, piceatannol, platycodin D, reproterol, ribavirin, riboflavin, rosmarinic acid, sildenafil, silybin, sugetriol-3,9-diacetate, sulfasalazine, tigecycline, valganciclovir, or β-thymidine.

The protease inhibitor may be lopinavir, ritonavir, or a combination thereof.

The RNA-dependent RNA polymerase inhibitor may be (R)-((1R,5aS,6R,9aS)-1,5a-dimethyl-7-methylene-3-oxo-6-((E)-2-(2-oxo-2,5-dihydrofuran-3-yl)ethenyl)decahydro-1H-benzo[c]azepin-1-yl)methyl 2-amino-3-phenylpropanoate, 14-deoxy-11,12-didehydroandrographolide, 14-hydroxycyperotundone, 2-((1R,5R,6R,8aS)-6-hydroxy-5-(hydroxymethyl)-5,8a-dimethyl-2-methylenedecahydronaphthalen-1-yl)ethyl benzoate, 2-(3,4-dihydroxyphenyl)-2-[[2-(3,4-dihydroxyphenyl)-3,4-dihydro-5,7-dihydroxy-2H-1-benzopyran-3-yl]oxy]-3,4-dihydro-2H-1-benzopyran-3,4,5,7-tetrol, 20,300-dihydroxy-3,4-seco-friedelolactone-27-lactone, 20-hydroxy-3, 4-seco-friedelolactone-27-oic acid, andrographiside, AT-511, AT-527, AT-9010, atovaquone, beclabuvir, benzylpenicilloyl G, betulonal, bromocriptine, ceftibuten, cefuroxime, chenodeoxycholic acid, chlorhexidine, cortisone, cromolyn, dabigatran etexilate, dasabuvir, deleobuvir, diphenoxylate, favipiravir, fenoterol, filibuvir, fludarabine, galidesivir, gnidicin, gniditrin, idarubicin, itraconazole, novobiocin, pancuronium bromide, penciclovir, phyllaemblicin B, ponatinib, radalbuvir, remdesivir, setrobuvir, silybin, sofosbuvir, sugetriol-3,9-diacetate, theaflavin 3,30-di-O-gallate, tegobuvir, tibolone, or valganciclovir, The virulence factor may be Nsp1, Nsp3c, or ORF7a.

The xanthine oxidase inhibitor may be allopurinol, oxypurinol, tisopurine, topiroxostat, phytic acid, or myoinositol.

For example and without limitation, the antiviral agent may target 3CLpro, ACE2, C-terminal RNA binding domain (CRBD), E-channel (E protein), helicase, RNA-dependent RNA polymerase, and Nsp1, Nsp3 (including one or more of Nsp3b, Nsp3c, PLpro, and Nsp3e), Nsp7-Nsp8 complex, Nsp9-Nsp10, and Nsp14-Nsp16, N-terminal RNA binding domain (NRBD), ORF7a, Spike, or TMPRSSS2.

Other types of antiviral agents and targets for antiviral agents that may be useful for treating infection with SARS-CoV-2 are described in Wu, et al., Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods, Acta Pharm Sin B, 2020 Feb. 27, doi: 10.1016/j.apsb.2020.02.008, the contents of which are incorporated herein by reference.

Anti-inflammatory agents include corticosteroids and non-steroidal anti-inflammatory drugs (NSAIDs). For example and without limitation, anti-inflammatory agents include acematricin, acetate, aloe vera extracts, alpha-methyl dexamethasone, amcinafide, arnica flower, asprin, beclamethasone dipropionate, benorylate, benoxaprofen, betamethasone and its esters, chloroprednisone, chloroprednisone acetate, clescinolone, clidanac, clobetasol valerate, clocortelone, comfrey root, desonide, desoxycorticosterone acetate, desoxymethasone, dexamethasone, dexamethasone phosphate, dichlorisone, dichlorisone, diclofenac, di-florasone diacetate, diflucortolone and its derivatives, difluprednate, disalacid, enolic acids, extracts from genus Commiphom (Commiphora mukul), extracts from genus Rubis (Rubia cordifolia), fenamic acid derivatives, fenclofenac, fenugreek seed, fluadrenolone, flubiprofen, flucloronide, flucortine butyl ester, flucrolone acetonide, flufenamic acid derivatives such as N-(α,α,α-trifluoro-m-tolyl) anthranilic acid), flunisolide, fluocinonide, fluocortolone, fluoromethalone, fluperolone, fluprednidine, fluprednisolone, flurandrenolone, furofenac, halcinonide, hydrocortamate, hydrocortisone, hydrocortisone acetate, hydrocortisone butyrate, hydrocortisone cyclopentylpropionate, hydrocortisone valerate, hydroxytriamcilone, indomethacin, isozepac, ketoprofen, matricarria flowers, meclofenamic acid derivatives (e.g. sodium meclofenamate), medrysone, mefenamic acid derivatives (e.g. N-(2,3-xyl-yl) anthranilic acid), meprednisone, methylprednisolone, naproxen, oxicams (e.g. piroxicam and isoxicam), oxyphenbutazone, paramethasone, phenylbutazone, prednisolone, prednisone, propionic acid esters such as ibuprofen, pyrazolidinediones, such as feprazone, safaprin, salicylic acid derivatives, sulfinpyrazone, sulindac, suprofen, tolmetin, triamcinolone acetonide, trimethasone, trisilate, willow bark, and zomepirac.

Combinations therapies may include two or more agents that have different mechanisms of action and/or are in different functional classes. For example and without limitation, the method may include one of the following combinations: a pyrimidine synthesis inhibitor and a purine synthesis inhibitor; and a pyrimidine synthesis inhibitor and an antiviral agent of another functional class, such as any of those described above.

Combination therapies may include multiple periods in which different agents or different combinations of agents are provided to the subject. Different agents or different combinations of agents may be provided concurrently, sequentially, in overlapping periods, in temporally separated periods, or in any other manner known to one of ordinary skill in the art. Exemplary temporal regimens for administering combination therapies are provided below.

For example and without limitation, and combination therapy may include a first period and a second period that follows the first period, the periods being as follows: a first period during which a first agent but not a second agent is provided to the subject and a second period during which the second agent but not the first agent is provided to the subject; a first period during which a first agent and a second agent are provided to the subject and a second period during which the second agent but not the first agent is provided to the subject; a first period during which a first agent but not a second agent is provided to the subject and a second period during which the first agent and the second agent are provided to the subject; and a first period during which first combination of agents is provided to the subject and a second period during which a second, different combination of agents is provided to the subject. In particular embodiments, brequinar or a pharmaceutically acceptable salt thereof is provided to the subject during a first period, and an anti-inflammatory agent is provided to the subject during a second period that follows the first period. Brequinar or a pharmaceutically acceptable salt thereof may be withheld from the subject during the second period. The anti-inflammatory may or may not be provided during the first period. Brequinar or a pharmaceutically acceptable salt thereof may be provided during the first period according to a dosing regimen, such as any of those described above. In combination therapies, different therapeutic agents may be provided in a single formulation. For example, a combination therapy may include providing brequinar or a pharmaceutically acceptable salt thereof in the same formulation as a second agent, such as an antiviral agent or anti-inflammatory agent. In some embodiments, brequinar or a pharmaceutically acceptable salt thereof and dexamethasone are provided in the same formulation.

Alternatively, in combination therapies, different therapeutic agents may be provided in separate formulations. For example, a combination therapy may include providing brequinar or a pharmaceutically acceptable salt thereof and a second agent, such as an antiviral agent or anti-inflammatory agent, in separate formulations. In some embodiments, brequinar or a pharmaceutically acceptable salt thereof and dexamethasone are provided in separate formulations.

Monitoring Metabolite Levels Methods of treating a condition in a subject may include monitoring the level of a metabolite, such as DHO, in a sample obtained from the subject. Monitoring the level of a metabolite may include receiving information about the measured level of the metabolite. Monitoring the level of a metabolite may include measuring the metabolite.

In some embodiments, the metabolite is measured by mass spectrometry, optionally in combination with liquid chromatography. Molecules may be ionized for mass spectrometry by any method known in the art, such as ambient ionization, chemical ionization (CI), desorption electrospray ionization (DESI), electron impact (EI), electrospray ionization (ESI), fast-atom bombardment (FAB), field ionization, laser ionization (LIMS), matrix-assisted laser desorption ionization (MALDI), paper spray ionization, plasma and glow discharge, plasma-desorption ionization (PD), resonance ionization (RIMS), secondary ionization (SIMS), spark source, or thermal ionization (TIMS). Methods of mass spectrometry are known in the art and described in, for example, U.S. Pat. Nos. 8,895,918; 9,546,979; 9,761,426; Hoffman and Stroobant, Mass Spectrometry: Principles and Applications (2nd ed.). John Wiley and Sons (2001), ISBN 0-471-48566-7; Dass, Principles and practice of biological mass spectrometry, New York: John Wiley (2001) ISBN 0-471-33053-1; and Lee, ed., Mass Spectrometry Handbook, John Wiley and Sons, (2012) ISBN: 978-0-470-53673-5, the contents of each of which are incorporated herein by reference.

In certain embodiments, a sample can be directly ionized without the need for use of a separation system. In other embodiments, mass spectrometry is performed in conjunction with a method for resolving and identifying ionic species. Suitable methods include chromatography, capillary electrophoresis-mass spectrometry, and ion mobility. Chromatographic methods include gas chromatography, liquid chromatography (LC), high-pressure liquid chromatography (HPLC), hydrophilic interaction chromatography (HILIC), ultra-performance liquid chromatography (UPLC), and reversed-phase liquid chromatography (RPLC). In a preferred embodiment, liquid chromatography-mass spectrometry (LC-MS) is used. Methods of coupling chromatography and mass spectrometry are known in the art and described in, for example, Holcapek and Brydwell, eds. Handbook of Advanced Chromatography/Mass Spectrometry Techniques, Academic Press and AOCS Press (2017), ISBN 9780128117323; Pitt, Principles and Applications of Liquid Chromatography-Mass Spectrometry in Clinical Biochemistry, The Clinical Biochemist Reviews. 30(1): 19-34 (2017) ISSN 0159-8090; Niessen, Liquid Chromatography-Mass Spectrometry, Third Edition. Boca Raton: CRC Taylor & Francis. pp. 50-90. (2006) ISBN 9780824740825; Ohnesorge et al., Quantitation in capillary electrophoresis-mass spectrometry, Electrophoresis. 26 (21): 3973-87 (2005) doi:10.1002/elps.200500398; Kolch et al., Capillary electrophoresis-mass spectrometry as a powerful tool in clinical diagnosis and biomarker discovery, Mass Spectrom Rev. 24 (6): 959-77. (2005) doi:10.1002/mas.20051; Kanu et al., Ion mobility-mass spectrometry, Journal of Mass Spectrometry, 43 (1): 1-22 (2008) doi:10.1002/jms.1383, the contents of which are incorporated herein by reference.

A sample may be obtained from any organ or tissue in the individual to be tested, provided that the sample is obtained in a liquid form or can be pre-treated to take a liquid form. For example and without limitation, the sample may be a blood sample, a urine sample, a serum sample, a semen sample, a sputum sample, a lymphatic fluid sample, a cerebrospinal fluid sample, a plasma sample, a pus sample, an amniotic fluid sample, a bodily fluid sample, a stool sample, a biopsy sample, a needle aspiration biopsy sample, a swab sample, a mouthwash sample, a cancer sample, a tumor sample, a tissue sample, a cell sample, a synovial fluid sample, a phlegm sample, a saliva sample, a sweat sample, or a combination of such samples. The sample may also be a solid or semi-solid sample, such as a tissue sample, feces sample, or stool sample, that has been treated to take a liquid form by, for example, homogenization, sonication, pipette trituration, cell lysis etc. For the methods described herein, it is preferred that a sample is from plasma, serum, whole blood, or sputum.

The sample may be kept in a temperature-controlled environment to preserve the stability of the metabolite. For example, DHO is more stable at lower temperatures, and the increased stability facilitates analysis of this metabolite from samples. Thus, samples may be stored at 4° C., −20° C., or −80° C.

In some embodiments, a sample is treated to remove cells or other biological particulates. Methods for removing cells from a blood or other sample are well known in the art and may include e.g., centrifugation, sedimentation, ultrafiltration, immune selection, etc.

The sample may be obtained from an individual before or after administration to the subject of an agent that alters activity of a metabolic pathway, such as inhibitor of an enzyme in the pathway. For example, the sample may be obtained 1 hour, 2 hours, 4 hours, 6 hours, 8 hours, 12 hours, 24 hours, 36 hours, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days or more before administration of an agent, or it may be obtained 1 hour, 2 hours, 4 hours, 6 hours, 8 hours, 12 hours, 24 hours, 36 hours, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days or more after administration of an agent.

The dosing regimen may be adjusted by comparing a measured level of a metabolite, e.g., DHO, in a sample obtained from a subject to a reference that provides an association between the measured level and a recommended dosage adjustment of brequinar. For example, the reference may provide a relationship between administration of the brequinar composition and levels of the metabolite in the subject. The relationship can be empirically determined from a known dose and time of administration of brequinar and measured levels of the metabolite at one or more subsequent time points. The reference may include a relationship between measured levels of brequinar or a metabolic product of brequinar and measured levels of the metabolite. Methods of dosing brequinar based on measured metabolite levels are known in the art and described in, for example, International Patent Publication Nos. WO 2019/191030 and WO 2019/191032, the contents of which are incorporated herein by reference.

From the comparison between the measured level of the metabolite and the reference, a dosing regimen may then be adjusted. For example, one or more of the dosages, intervals between doses, and dosage-free periods may be adjusted.

The dosing regimen may ensure that levels of a metabolite, such as DHO, are raised or maintained at a minimum threshold required to achieve a certain effect. For example, the dosing regimen may raise or maintain levels of the metabolite above a threshold level in the subject for a certain time period. The time period may include a minimum, a maximum, or both. For example, the dosing regimen may raise or maintain levels of the metabolite above the threshold level for at least 6 hours, 12, hours, 24 hours, at least 48 hours, at least 60 hours, at least 72 hours, at least 84 hours, at least 96 hours, at least 5 days, at least 6 days, at least 7 days, at least 10 days, at least 2 weeks, or more. The dosing regimen may raise or maintain levels of the metabolite above the threshold level for not more than 24 hours, not more than 36 hours, not more than 48 hours, not more than 60 hours, not more than 72 hours, not more than 84 hours, not more than 96 hours, not more than 5 days, not more than 6 days, not more than 7 days, not more than 10 days, or not more than 2 weeks. The dosing regimen may raise or maintain levels of the metabolite above the threshold level for at least 72 hours but not more than 96 hours, for at least 72 hours but not more than 5 days, for at least 72 hours but not more than 6 days, for at least 72 hours but not more than 7 days, for at least 96 hours but not more than 7 days.

The dosing regimen may ensure that levels of a metabolite, such as DHO, do not exceed or are maintained below a maximum threshold that is associated with toxicity. Levels of the metabolite above a maximum threshold may indicate that brequinar is causing or is likely to cause an adverse event in the subject. For example and without limitation, adverse events include abdominal pain, anemia, anorexia, blood disorders, constipation, diarrhea, dyspepsia, fatigue, fever, granulocytopenia, headache, infection, leukopenia, mucositis, nausea, pain at the injection site, phlebitis, photosensitivity, rash, somnolence, stomatitis, thrombocytopenia, and vomiting.

The dosing regimen may include a time point for administration of one or more subsequent doses to raise or maintain levels of the metabolite, such as DHO, above a threshold level for a certain time period. The time point for administration of a subsequent dose may be relative to an earlier time point. For example, the time point for administration of a subsequent dose may be relative to a time point when a previous dose was administered or a time point when a sample was obtained from a subject.

Minimum and maximum threshold levels of a metabolite depend on a variety of factors, such as the metabolites and type of sample. Minimum and maximum threshold levels may be expressed in absolute terms, e.g., in units of concentration, or in relative terms, e.g., in ratios relative to a baseline or reference value. For example, the minimum threshold (below which a patient may receive a dose increase or additional dose) could also be calculated in terms of increase from a pre-treatment DHO level or baseline level.

Minimum threshold levels of DHO or orotate in a human plasma sample may be about 0 ng/ml, about 10 ng/mL, about 20 ng/mL, about 50 ng/mL, about 100 ng/mL, about 150 ng/mL, about 200 ng/mL, about 250 ng/mL, about 300 ng/mL, about 350 ng/mL, about 400 ng/mL, about 450 ng/mL, about 500 ng/mL, about 550 ng/mL, about 600 ng/mL, about 650 ng/mL, about 700 ng/mL, about 750 ng/mL, about 800 ng/mL, about 850 ng/mL, about 900 ng/mL, about 950 ng/mL, about 1000 ng/mL, about 1250 ng/ml, about 1500 ng/ml, about 1750 ng/ml, about 2000 ng/ml, about 2500 ng/ml, about 3000 ng/ml, about 3500 ng/ml, about 4000 ng/ml, about 4500 ng/ml, about 5000 ng/ml, about 6000 ng/ml, about 8000 ng/ml, about 10,000 ng/ml, about 12,000 ng/ml, about 15,000 ng/ml, about 20,000 ng/ml, about 25,000 ng/ml, about 30,000 ng/ml, about 40,000 ng/ml, about 50,000 ng/ml, about 75,000 ng/ml, about 100,000 ng/ml, about 150,000 ng/ml, about 200,000 ng/ml, about 300,000 ng/ml, or about 400,000 ng/ml. The minimum threshold may include any value that falls between the values recited above. Thus, the minimum threshold may include any value between 0 ng/ml and 400,000 ng/ml.

Maximum threshold levels of DHO or orotate in a human plasma sample may be about 50 ng/mL, about 100 ng/mL, about 150 ng/mL, about 200 ng/mL, about 250 ng/mL, about 300 ng/mL, about 350 ng/mL, about 400 ng/mL, about 450 ng/mL, about 500 ng/mL, about 550 ng/mL, about 600 ng/mL, about 650 ng/mL, about 700 ng/mL, about 750 ng/mL, about 800 ng/mL, about 850 ng/mL, about 900 ng/mL, about 950 ng/mL, about 1000 ng/mL, about 1250 ng/ml, about 1500 ng/ml, about 1750 ng/ml, about 2000 ng/ml, about 2500 ng/ml, about 3000 ng/ml, about 3500 ng/ml, about 4000 ng/ml, about 4500 ng/ml, about 5000 ng/ml, about 6000 ng/ml, about 8000 ng/ml, about 10,000 ng/ml, about 12,000 ng/ml, about 15,000 ng/ml, about 20,000 ng/ml, about 25,000 ng/ml, about 30,000 ng/ml, about 40,000 ng/ml, about 50,000 ng/ml, about 75,000 ng/ml, about 100,000 ng/ml, about 150,000 ng/ml, about 200,000 ng/ml, about 300,000 ng/ml, about 400,000 ng/ml, or about 500,000 ng/ml. The maximum threshold may include any value that falls between the values recited above. Thus, the maximum threshold may include any value between 50 ng/ml and 500,000 ng/ml.

The minimum threshold of DHO or orotate may be about 1.5 times the baseline level, about 2 times the baseline level, about 2.5 times the baseline level, about 3 times the baseline level, about 4 times the baseline level, about 5 times the baseline level, about 10 times the baseline level, about 20 times the baseline level, about 50 times the baseline level, about 100 times the baseline level, about 200 times the baseline level, about 500 times the baseline level, about 1000 times the baseline level, about 2000 times the baseline level, or about 5000 times the baseline level. The minimum threshold may include any ratio that falls between those recited above. Thus, the minimum threshold may be any ratio between 1.5 times the baseline level and 5000 times the baseline level.

The maximum threshold of DHO or orotate may be about 2 times the baseline level, about 2.5 times the baseline level, about 3 times the baseline level, about 4 times the baseline level, about 5 times the baseline level, about 10 times the baseline level, about 20 times the baseline level, about 50 times the baseline level, about 100 times the baseline level, about 200 times the baseline level, about 500 times the baseline level, about 1000 times the baseline level, about 2000 times the baseline level, about 5000 times the baseline level, or about 10,000 times the baseline level. The maximum threshold may include any ratio that falls between those recited above. Thus, the maximum threshold may be any ratio between 2 times the baseline level and 10,000 times the baseline level.

Dosage of brequinar also depends on factors such as the type of subject and route of administration. The dosage may fall within a range for a given type of subject and route of administration, or the dosage may be adjusted by a specified amount for a given type of subject and route of administration. For example, dosage of brequinar for oral or intravenous administration to a subject, such as human or mouse, may be about 1 mg/kg, about 2 mg/kg, about 5 mg/kg, about 7.5 mg/kg, about 10 mg/kg, about 15 mg/kg, about 20 mg/kg, about 25 mg/kg, about 50 mg/kg, about 75 mg/kg, or about 100 mg/kg. Dosage of brequinar for oral or intravenous administration to a subject, such as a human or mouse, may be adjusted by about 1 mg/kg, about 2 mg/kg, about 5 mg/kg, about 7.5 mg/kg, about 10 mg/kg, about 15 mg/kg, about 20 mg/kg, about 25 mg/kg, or about 50 mg/kg. Dosage of brequinar for oral or intravenous administration to an animal subject, such as a human or mouse, may be about 50 mg/m², about 100 mg/m², about 200 mg/m², about 300 mg/m², about 350 mg/m², about 400 mg/m², about 500 mg/m², about 600 mg/m², about 700 mg/m², about 750 mg/m², about 800 mg/m², or about 1000 mg/m². Dosage of brequinar for oral or intravenous administration to an animal subject, such as a human or mouse, may be adjusted by about 50 mg/m², about 100 mg/m², about 200 mg/m², about 300 mg/m², about 350 mg/m², or about 400 mg/m².

Methods may include determining whether the level of the metabolite is within a threshold range (e.g., above a minimal threshold and/or below a potential toxicity threshold) that warrants dosing, and/or that warrants dosing at a particular level or in a particular amount. Methods of determining the level of a metabolite and adjusting brequinar dosing regimen based on the determined levels of the metabolite are known in the art and described in, for example, International Patent Publication Nos. WO 2019/191030 and WO 2019/191032, the contents of which are incorporated herein by reference.

The methods may include providing at least one dose of brequinar to a subject whose plasma metabolite level has been determined and is below a pre-determined threshold (e.g., a pre-determined potential toxicity threshold and/or a pre-determined potential efficacy threshold). The predetermined threshold reflects percent inhibition of DHODH in the subject relative to a baseline determined for the subject. The baseline may be determined by an assay.

In order to maintain inhibition of DHODH at an effective threshold, multiple doses of brequinar may be administered to the subject. Dosing of brequinar may occur at different times and in different amounts. The present disclosure encompasses those methods that can maintain inhibition of the target enzyme at a consistent level at or above the efficacy threshold throughout the course of treatment. In some embodiments, the amount of inhibition of DHODH is measured by the amount of metabolite in the plasma of a subject.

The method may comprise a step of re-determining the subject's plasma metabolite level after administration of at least one dose. In some embodiments, the subject's plasma metabolite level is re-determined after each dose. The method may comprise administering at least one further dose of brequinar after the subject's plasma metabolite level has been determined again (e.g., after administering a first or previous dose) to be below the pre-determined threshold. If the subject's plasma metabolite level is determined to be above a pre-determined threshold, dosing can be discontinued. Thus, no further dose of brequinar is administered until the subject's plasma metabolite level has been determined to again be below a pre-determined threshold.

EXAMPLES Example 1: Determining Brequinar Levels in Plasma

FIG. 4 is a scatter plot illustrating the concentration of brequinar in subject plasma over time when administered twice weekly.

FIG. 5 is a scatter plot illustrating the bioavailability of an IV formulation of brequinar as compared to an oral dosage form.

The concentration of DHO in a subject's plasma is correlated with the concentration of DHODH inhibitor in the plasma. As provided herein, the disclosed methods provide, in some embodiments, administering the DHODH inhibitor when the DHO concentration in the plasma is either at least a particular efficacy threshold or below a potential toxic threshold (i.e., a pre-determined level).

FIG. 6 is a scatter plot illustrating the concentration of brequinar in mice at a dose of 50 mg/kg over time. The dashed line illustrates that about 100 ng/mL concentration of DHO remains in the plasma at about 84 hours.

Example 2: Adverse Events Observed in Subjects Receiving Brequinar

Brequinar was administered intravenously to 209 subjects once a week with a median number of doses per patient of 4 (range 1 to 24) at a median dose of 1200 mg/m² (range 588 to 3110). Adverse events that were observed in more than 3% of subjects are reported in Table 4, below:

TABLE 4 No. of Patients Experiencing No. of the AE, 5 y Max Grade Patients Percent 1 2 3 4 All Body Systems 202 95.7 36 76 55 35 Thrombocytopenia 94 45.0 26 31 16 21 Nausea 91 43.5 59 19 12 1 Anemia 90 43.1 14 48 23 5 Diarrhea 77 36.8 43 21 10 3 Vomit 73 34.9 32 24 12 5 Leukopenia 69 33.0 26 31 10 2 Stomatitis 60 28.7 32 20 7 1 Rash 53 25.4 26 15 9 3 Mucositis 52 24.9 23 15 11 3 Granulocytopenia 37 19.6 16 17 3 5 Fatigue 33 15.8 23 8 2 0 Pain Inject Site 24 11.5 24 0 0 0 Anorexia 15 7.2 11 3 1 0 Fever 11 5.3 4 7 0 0 Constipation 10 4.8 6 2 1 0 Somnolence 9 4.3 7 2 0 0 Pain, Abdominal 8 3.8 4 3 1 0 Dyspepsia 7 3.3 6 1 0 0 Headache 7 3.3 4 3 0 0 Infection 7 3.3 4 3 0 0

Example 3: Determining DHO Levels in Plasma Samples Using DHO as a Standard

Prior to analysis the plasma samples are deproteinized by centrifugation through a 50 kD Amicon ultrafilter. 10 μL of a plasma sample is spiked with 5 μL of a standard solution of (S)-4,5-dihydroorotic-4,5,6-carboxy-¹³C4 acid (¹³C4-DHO) and then diluted with 35 μL of 0.1% (w/w) formic acid. Samples are injected into a reverse-phase 4 μm C18 column (Synergy Hydro RP-80A, 3 μm, 150×3 mm; Phenomenex, Australia). Chromatography is performed at 30° C. with a total flow rate of 0.3 mL/min, using solvent A (aqueous 5 mM ammonium acetate, 0.05% (w/v) formic acid) and solvent B (0.05% (w/v) formic acid in methanol) in a linear gradient elution from A:B 98:2 (v/v) to 85:15 (v/v) over 11 minutes, the 40:60 (v/v) for 1 minute, before returning to initial conditions for a further 6 minutes of equilibration.

Tandem mass spectrometry (LC/MS/MS) is performed using an Applied Biosystems API 4000 QTRAP mass spectrometer equipped with a Turbo-V-Spray source with the gas temperature set at 500° C. The source operated an electrospray interface (ESI) with switching ionization polarity (between +5000 V and −4000 V) during the run (18 min). The eluent is monitored by specific ion transitions for DHO and the internal standard. All data is quantified using Applied Biosystems software.

Example 4: Determining DHO Acid Levels in Plasma Samples Using Orotic Acid as a Standard

Prior to analysis the plasma samples are deproteinized by centrifugation through a 50 kD Amicon ultrafilter. 10 μL of a plasma sample is spiked with 5 μL of a standard solution of 15N2-orotic acid and then diluted with 35 μL of 0.1% (w/w) formic acid. Samples are injected into a reverse-phase 4 μm C18 column (Synergy Hydro RP-80A, 3 μm, 150×3 mm; Phenomenex, Australia). Chromatography is performed at 30° C. with a total flow rate of 0.3 mL/min, using solvent A (aqueous 5 mM ammonium acetate, 0.05% (w/v) formic acid) and solvent B (0.05% (w/v) formic acid in methanol) in a linear gradient elution from A:B 98:2 (v/v) to 85:15 (v/v) over 11 minutes, the 40:60 (v/v) for 1 minute, before returning to initial conditions for a further 6 minutes of equilibration.

Tandem mass spectrometry (LC/MS/MS) is performed using an Applied Biosystems API 4000 QTRAP mass spectrometer equipped with a Turbo-V-Spray source with the gas temperature set at 500° C. The source operated an electrospray interface (ESI) with switching ionization polarity (between +5000 V and −4000 V during the run (18 min). The eluent is monitored by specific ion transitions for DHO and the internal standard. All data was quantified using Applied Biosystems SCIEX Multiquant software.

Example 5: Determined DHO Levels in Healthy Subjects and Cancer Patients

The concentration of dihydroorotic acid in human K2EDTA plasma samples was determined by reversed-phase high performance liquid chromatography with tandem mass spectrometric detection (LC-MS/MS). Plasma samples (50 μL) were spiked with 5 μL of a 1.0 μg/mL solution of (S)-4,5-dihydroorotic-4,5,6,carboxy-¹³C4 acid (¹³C4-DHO) in water, which was used as the internal standard (IS), then vigorously mixed with acetonitrile (200 μL) for 5 min. After centrifugation (12,000 rpm, 5 min), 150 μL of the supernatant was applied to a preconditioned Waters (Milford, Mass.) Oasis MAX solid phase extraction cartridge (1 cc, 30 mg). The cartridge was washed sequentially with water and methanol before eluting the analyte with 1% (v/v) formic acid in methanol (1 mL). The eluent was evaporated under a stream of nitrogen and reconstituted in 50 μL of 1% (v/v) formic acid in water. The solution was transferred into a conical bottom insert placed in an amber autosampler vial and sealed. A 10 μL aliquot of the solution was injected onto a Phenomenex (Torrance, Calif.) Synergi 4 μm Hydro-RP 80A HPLC column (250 mm×3.0 mm i.d.) preceded by an AQ C18 guard cartridge (4.0 mm×3.0 mm i.d.) and separated using an isocratic mobile phase composed of 0.05% (v/v) formic acid in water at a flow rate of 0.5 mL/min. An Agilent Technologies (Santa Clara, Calif.) model G6410B triple quadrupole mass spectrometer with an electrospray ionization interface was used for detection. Nitrogen was used as the nebulizing gas (30 p.s.i.) and drying gas (10 L/min, 350° C.). With a transfer capillary potential of 1,500 V, negative ions resulting from the m/z 157-113 transition for dihydroorotic acid and the m/z 161→117 transitions for the IS were measured by multiple reaction monitoring (dwell time, 150 msec; fragmentor potential, 70 V; collision energy, 4 V; collision cell accelerator voltage, 4 V). Quantitation was based upon integrating the extracted ion chromatograms for both transitions to provide peak areas and calculating the ratio of the analyte peak area to the IS peak area for each sample.

Table 5 provides data of DHO concentration for samples from certain random cancer patients, samples from healthy subjects, and samples from mice.

TABLE 5 ASSAY DHO AVG. ASSAY Subject No. Sample CONC. ng/mL CONC. ng/mL Cancer Patients 1 1 4.1 2 4.25 4.18 2 1 0 2 0 0.00 3 1 1.17 2 0.19 0.68 4 1 15.1 2 15.4 15.25 5 1 5.2 2 5.3 5.25 6 1 0.41 2 0.86 0.64 Healthy Subjects 1 1 0 2 0 0.00 2 1 0 2 0 0.00 3 1 0 2 0 0.00 4 1 0 2 0 0.00 5 1 0 2 0 0.00 6 1 0 2 0 0.00 Mice 1 1 1 1 2 0.06 0.00

Table 6 provides patient data for 20 anonymous cancer patients whose DHO acid concentration was measured.

TABLE 6 Blast Inunmiophe- Inunmiophe- Diag- Gen- Form and Cells by notyping notyping No. nosis Sample der Age Stage Chemotherapy Morphology* CD34⁺* CD19⁺/CD5⁺* Cytogenetics 1 AML Blood & F 60 M0 or M5a 12.6 (BM) 45, XX, −3, der(5)t(5; Marrow 3)(ql3; ql2), −7, inv(12)(p 11, 2q24.1), dic(13; 22)(p 12; p 12), +l~2mar[8]/46, XX1121 2 AML 3 AML Blood M 84 Untreated 30-40 (BM) 1.64 (PB)/ 43.1 (BM) 4 AML 5 AML 6 AML Blood M 35 Tretinoin 65 (PB)/ 39 (PB) 43 (BM) 7 AML Blood F 37 M3 Tretinoin 75 (PB)/ 0.1 Idarubicin 79 (BM) Arsenic trioxide 8 AML Blood M 68 60 (BM) 11 (PB) 9 AML Blood M 70 76 (BM) 97 (PB) ish(D7Zlx2, D7S486xl)[41/200], (KAT6Ax3)[461/500], (D8Z2, MYC)x3 [186/200], (RLINXlTlx3)[461/5001 10 AML Blood & F 57 Relapsed Retinoic 0 (PB)/ 0.7 (PB) t(15; 17) PML/RARA Marrow acid, 11 (BM) fusion [by FISH]) Arsenic, Abnormal 918″ Idarubicin, Arsenic 11 AML Blood M 65 non 38 (BM) 0.77 (PB) FLT3/NPM1 mutations promyelocytic with monocytic differentiation 12 CLL Blood & M 53 97 (PB)/ Marrow 91 (BM) 13 CLL Blood M 75 Relapsed 85 (PB)/ 7.5% have 75 (BM) del[13q/14]- specific signal 14 CLL Blood & F 56 Relapsed Rituxan 27.7 (PB)/ Marrow refractory 67.5 (BM) 15 CLL Blood & F 67 Relapsed 53.4 (PB)/ Marrow 61.4 (BM) 16 CLL Blood F 69 3.73 (PB) 17 CML 18 CML Blood & M 50 Newly 0.8 (PB)/ BCR-ABL Marrow Diagnosed, 1.4 (BM) positive Chronic Phase 19 CML Blood & M 31 Relapsed BCR-ABL, 0.72 (PB)/ Marrow refractory Gleevec 7.1 (BM) 20 CML Blood & M Newly N/A 1.6 (PB)/ BCR-ABL Marrow diagnosed 1.8 (BM) positive chronic phase *(PB = % Blood, BM % Marrow)

Table 7 provides baseline endogenous DHO acid concentration in plasma samples from the set of 20 cancer patients.

TABLE 7 No. Assay 1 Assay 2 Assay 3 Mean 1 <LOD <LOD <LLQ 2 13.8 15.2 14.5 3 58.1 49.0 53.6 4 32.8 30.0 31.4 5 <LOD <LLQ <LLQ 6  9.5  8.4  8.99 7 <LLQ <LLQ <LLQ 8 18.0 16.4 17.2 9   6.7^(b) 33.4 29.9 31.6 10 12.8 13.9 13.4 11  17.0^(b) 11.8 10.2 11.0 12 <LOD <LOD <LLQ 13 <LOD <LOD <LLQ 14 <LOD <LOD <LLQ 15  6.51  5.14  5.83 16 <LLQ <LLQ <LLQ 17  37.1^(b) <LOD <LOD <LLQ 18 <LOD <LLQ <LLQ 19 <LOD <LOD <LLQ 20   5.1^(b) <LLQ <LLQ <LLQ ^(a)<LOD, below the limit of detection (analyte peak not distinguishable from baseline); <LLQ, assayed concentration below the lower limit of quantitation (5.0 ng/mL). ^(b)Result not used for calculation of the mean assayed concentration and percent difference.

FIG. 7 is a scatter plot illustrating the baseline DHO levels in random cancer patients and healthy patients, as reported in Table 5.

Example 6: Clinical Dosing Regimens Previously Tested for Brequinar in Patients with Refractory Solid Tumors

Previous clinical dosing regimens assessed brequinar for use in treating refractory solid tumors in patients. For example, Arteaga reported administration of brequinar as “single daily i.v. bolus over a 5-day period repeated every 28 days.” Arteaga, et al., “Phase I clinical and pharmacokinetic trial of Brequinar sodium (DuP 785; NSC368390),” Cancer Res., 49(16):4648-4653 (Aug. 15, 1989). Specifically, Arteaga administered “one hundred seven courses of treatment at dosages ranging from 36 to 300 mg/m²/day×5” to 45 patients (31 male and 14 female) with refractory solid tumors. The reported median age of these patients was 58 years (range 30-74); and the median Southwest Oncology Group performance status was reported to be 1 (range, 0-3). Arteaga found “for the daily×5 i.v. schedule, the recommended dose of Brequinar for phase II evaluation is 250 mg/m² for good risk patients and 135 mg/m² for poor risk patients.”

Burris reported “investigating the pharmacokinetic and toxicity of brequinar in combination with cisplatin” where patients were initially treated with weekly brequinar, in combination with an every-three-week administration of cisplatin. See Burris, et al., “Pharmacokinetic and phase I studies of brequinar (DUP 785; NSC368390) in combination with cisplatin in patients with advanced malignancies,” Invest. New Drugs, 16(1):19-27 (1998). Burris found that “due to toxicity, the schedule was modified to a 28-day cycle with brequinar given on days 1, 8, 15, and cisplatin on day 1.” A total of 24 patients (16 male, 8 female; median age 57; median performance status 1) received 69 courses of therapy. Six dose levels were explored, with cisplatin/brequinar doses, respectively, of 50/500, 50/650, 50/860, 60/860, 75/650, and 75/860 mg/m². Burris concluded that “full dose of 75 mg/m² cisplatin (day 1) can be administered with 650 mg/m² brequinar (days 1, 8 and 15) without significant modifications of individual drug pharmacokinetic parameters.”

Noe reported “in vitro and in vivo studies [of brequinar] demonstrate the superiority of prolonged drug exposure in achieving tumor growth inhibition. This phase I study evaluated the administration of brequinar sodium by short, daily i.v. infusion for 5 days repeated every 4 weeks.” See Noe, et al., “Phase I and pharmacokinetic study of brequinar sodium (NSC368390),” Cancer Res., 50(15):4595-4599 (1990). Noe examined “fifty-four subjects . . . received drug in doses ranging from 36-300 mg/m².” Noe found that “the maximum tolerated dose on the ‘daily times 5’ schedule was 300 mg/m²” and that “the recommended phase II dose is 250 mg/m².” Noe concluded that “pharmacodynamic analysis of the day 1 kinetic parameters and the toxicities occurring during the first cycle of drug therapy revealed significant correlations between mucositis and dose, AUC, and peak brequinar concentration; between leukopenia and AUC and peak drug concentration; and between thrombocytopenia and beta elimination rate.”

Schwartsmann reported dosing brequinar in 43 patients who “received 110 courses of Brequinar sodium by short-term intravenous (i.v.) infusion 38 every 3 weeks.” See Schwartsmann, et al., “Phase I study of Brequinar sodium (NSC 368390) in patients with solid malignancies,” Cancer Chemother. Pharmacol., 25(5):345-351 (1990). Schrwatsmann based dose escalation on “a modified Fibonacci scheme,” initially, but relied on a pharmacologically guided dose escalation after PK data became available, noting that “at toxic levels, dose escalation was applied on the basis of clinical judgement.” Swchwartsmann reported that “[t]he maximum tolerable doses for poor- and good-risk patients were 1,500 and 2,250 mg/m², respectively. One mixed response was observed in a patient with papillary carcinoma of the thyroid. The recommended doses for phase II studies are 1,200 and 1,800 mg/m² Brequinar sodium, given by a 1-h i.v. infusion every 3 weeks to poor- and good-risk patients, respectively.”

Example 7: Exemplary Clinical Dosing in Accordance with the Present Disclosure Inclusion Criteria

The following are proposed inclusion criteria for subjects in a proposed clinical trial:

-   -   Willing and able to provide written informed consent for the         trial.     -   Adults, 18 years of age and older, with pathologically         confirmed, relapsed or refractory acute myelogenous leukemia.     -   ≥18 years of age on day of signing informed consent     -   ECOG Performance Status 0 to 2.     -   Cardiac ejection fraction ≥40%     -   Adequate hepatic function (unless deemed to be related to         underlying leukemia)     -   Direct bilirubin ≤2×ULN     -   ALT ≤3×ULN     -   AST≤3×ULN     -   Adequate renal function as documented by creatinine clearance         ≥30 mL/min based on the Cockcroft-Gault equation

In the absence of rapidly proliferative disease, the interval from prior leukemia directed therapy to time of study initiation will be at least 7 days for cytotoxic or non-cytotoxic (immunotherapy) agents. Hydrea is allowed up to 48 hours prior to the first dose for patients with rapidly proliferative disease.

The effects of brequinar on the developing human fetus are unknown. For this reason, women of child-bearing potential and men must agree to use adequate contraception (hormonal or barrier method of birth control; abstinence) prior to study entry and for the duration of study participation. Should a woman become pregnant or suspect she is pregnant while she or her partner is participating in this study, she should inform her treating physician immediately. Men treated or enrolled on this protocol must also agree to use adequate contraception prior to the study, for the duration of study participation, and for 90 days after completion of brequinar administration.

Male subjects must agree to refrain from sperm donation from initial study drug administration until 90 days after the last dose of study drug.

Exclusion Criteria

The following are proposed exclusion criteria for excluding a subject in the study.

-   -   White blood count >25×109/L (note: hydroxyurea is permitted to         meet this criterion).     -   Any concurrent uncontrolled clinically significant medical         condition, laboratory abnormality, or psychiatric illness that         could place the participant at unacceptable risk of study         treatment.     -   QTc interval using Fridericia's formula (QTcF) ≥470 msec.         Participants with a bundle branch block and prolonged QTc         interval may be eligible after discussion with the medical         monitor.     -   The use of other chemotherapeutic agents or anti-leukemic agents         is not permitted during study with the following exceptions:     -   Intrathecal chemotherapy for prophylactic use or maintenance of         controlled CNS leukemia.     -   Use of hydroxyurea may be allowed during the first 2 weeks of         therapy if in the best interest of the participant and is         approved by the medical monitor.     -   AML relapse less than 6 months following stem cell         transplantation.     -   Presence of graft versus host disease (GVHD) which requires an         equivalent dose of ≥0.5 mg/kg/day of prednisone or therapy         beyond systemic corticosteroids (e.g. cyclosporine or other         calcineurin inhibitors or other immunosuppressive agents used         for GVHD).     -   Active cerebrospinal involvement of AML.     -   Diagnosis of acute promyelocytic leukemia (APL)     -   Clinically active hepatitis B (HBV) or hepatitis C (HCV)         infection.     -   Severe gastrointestinal or metabolic condition that could         interfere with the absorption of oral study medication     -   Prior malignancy, unless it has not been active or has remained         stable for at least 5 years. Participants with treated         non-melanoma skin cancer, in situ carcinoma or cervical         intraepithelial neoplasia, regardless of the disease-free         duration, are eligible if definitive treatment for the condition         has been completed. Participants with organ-confined prostate         cancer with no evidence of recurrent or progressive disease are         eligible if hormonal therapy has been initiated or the         malignancy has been surgically removed or treated with         definitive radiotherapy.     -   Nursing women or women of childbearing potential (WoCBP) with a         positive urine pregnancy test.

Dose Levels

Proposed dosing levels are provided below:

Patients are dosed every 3.5 days. An example schedule of events is reported in Table 8.

TABLE 8 Dose Escalation Maintenance Dose Cycle (Cycle 2 and (no dose adjustment) F/U Cycle 1 (Study Days 1-14) beyond as needed) Every 2 weeks Phone Call Day Day Day Day Day Day Day Day Final Final Visit + Procedures^(a) Screen^(b) 1 2 3 4 8 1 8 1 Visit 2 wks Survival Informed Consent X AE/Concomitant X X X X X X X X X X X Medication Assessment Demographics^(c) X Physical Exam (including X X X X X weight) Vital Signs^(c) X X X X X X X Pregnancy Test^(d) X X X ECOG Performance Status X Hematology/Chemistry^(e) X X X X X X X Chromosomal & X mutational testing^(f) 12-lead ECG X X X MIGA/Echocardiogram X Bone Marrow Sampling^(g) X X  X^(g) X Brequinar/DHO X X X X X X X X X Plasma Sample^(h) Ship Plasma Samples X X X Dispense/Collect X X X X Study Medication Dispense/Collect X X X X Subject Calendar/Diary Survival Assessment X ^(a)Visit window of ±1 day for dose escalation cycles; window of ±3 days for non-dose-escalation cycles. ^(b)Obtain informed consent prior to performing any screening or study-specific procedures. Screening procedures must be performed within 14 days prior to initial study drug administration. Procedures at C1D1 that are repeats of Screening may be omitted if <72 h since Screening assessment. ^(c)Demographic information includes date of birth, height, weight, race, and ethnic origin. Vital signs include heart rate, respiratory rate, seated blood pressure, oral/aural body temperature. ^(d)For women of childbearing potential only. ^(e)CBC differential may be omitted if previous WBC < 0.5 × 10⁹/L ^(f)Per institutional standard of care. ^(g)Local bone marrow sampling (core biopsy and aspirate) will include molecular testing, flow cytometry for minimal residual disease counts (MRD); perform bone marrow sampling at screening, once at C2D8 +/− 7 days, at Day 42, and once every 12 weeks after a stable dose has been reached. Only the Day 43 sample will be used to assess hematological toxicity. Ship sample to central lab for future testing. Timing of this procedure may be adjusted to ensure results are available for the next clinic visit. ^(h)Brequinar/DHO plasma sampling schedule: Cycle 1: 0 (pre-dose), post dose 1, 2, 4, 6, 24, 48, 72 hours and C1D8 pre-dose (+84 h after C1D4 dose); Cycle 2 and adjustment cycles: pre-dose Days 1 and 8. Maintenance dose: Day 1 pre-dose. Day 1 PK window ±15 minutes through 6 h draw, window for additional Cl draws ±2 h; window for Cycle 2 and beyond plasma brequinar/DHO draws ±4 h. Plasma samples for brequinar/DHO for expansion cohort are to be obtained prior to dosing on Day 1 of each 2-week cycle.

Another example dosing schema is:

Dose level Brequinar (mg/m²) +2 (Target dose) 800 +2 (Target dose) 650 0 (Starting dose) 500 −1 425 The dosing sequence (i.e. every 3.5 days) will be subject to revision after review of preliminary efficacy, toxicity, and PK data within this clinical trial. PK data from patients treated at dose level 0 will be used to evaluate the anticipated minimally effective dose, to adjust the dose and schedule, if necessary, in subsequent dose level cohorts.

Example 8: Determining Analyte Levels in Plasma

The following assay protocol is useful for measuring the concentration of analytes such as pyrazofurin, orotate (i.e., orotate), orotidylate monophosphate (OMP), and uradilyate monophosphate (UMP) in serum samples of subjects.

Prior to analysis 25 μL plasma samples are deproteinized by extraction with a 200 μL of 70:30 acetonitrile:methanol containing 1% formic acid and 1 μg/mL of the internal standard adenosine monophosphate (AMP). The acetonitrile:methanol solution is evaporated at 50° C. with nitrogen and reconstituted with 150 μL of water for injection. Samples are injected into a reverse-phase Waters Atlantis T3 2.1 mm×100 mm, 3 μm column. Chromatography is performed, using solvent A (aqueous 10 mM ammonium acetate, pH 4.8) and solvent B (0.1% (w/v) formic acid in methanol) in a linear gradient elution from A:B 98:2 (v/v) to 85:15 (v/v) over 11 minutes, the 40:60 (v/v) for 1 minute, before returning to initial conditions for a further 6 minutes of equilibration.

Tandem mass spectrometry (LC/MS/MS) is performed using an Applied Biosystems API 5000 QTRAP mass spectrometer equipped with a Turbo-V-Spray source with the gas temperature set at 500° C. The source operated an electrospray interface (ESI) with switching ionization polarity (between +5000 V and −4000 V) during the run (18 min). The eluent is monitored by specific ion transitions for DHO and the internal standard. All data is quantified using Applied Biosystems software.

Example 9: Concentration of Analyte Associated with Administration of OMP Decarboxylase Inhibitor

An OMP decarboxylase inhibitor, pyrazofurin was administered to mice by oral gavage. The concentration (ng/mL) of analytes selected from pyrazofurin (PYR), orotic acid (i.e., orotate), orotidylate monophosphate (OMP), and uradilyate monophosphate (UMP) in the serum samples were measured according to the assay methods reported in Example 1. The results are reported in Table 9:

TABLE 9 Source PYR 1 μM PYR 0.25 μM Cells Cells Cells Supe* Cells Cells Cells Supe* Time (hr) 1 hr 4 hr 24 hr 24 hr 1 hr 4 hr 24 hr 24 hr Orotate ng/mL 339 1170 1220 10005 231 758 1560 11300 OMP ng/mL 0 10 11 43 0 0 13 49 UMP ng/mL 552 408 326 69 737 474 548 67 PYR ng/mL 0 0 0 1010 0 0 0 273 *Supernatant

FIG. 8 is a scatter plot illustrating the concentrations of pyrazofurin and orotate in murine plasma over time when pyrazofurin is administered as a single dose (20 mg/kg).

FIG. 9 is a scatter plot illustrating the concentrations of pyrazofurin and orotate in murine plasma over time when pyrazofurin is administered as a single dose (20 mg/kg) on a log scale.

Example 10: Prior Dosing Regimens

Ohnuma and Holland reported an initial clinical study with pyrazofurin, where twenty-five patients with inoperable carcinoma and lymphoma were given pyrazofurin (PF) “by iv bolus at a dose level ranging from 100 to 300 mg/m² of estimated body surface area.” Further, “five patients with acute leukemia were given [pyrazofurin] by infusion at doses ranging from 250 mg/m²/24 hours to 1500 mg/m²/144 hours.” Ohnuma and Holland found that pyrazofurin “was well tolerated by most patients at doses of 100 mg/m² given as an iv bolus weekly or 250 mg/m² given every 2-3 weeks,” but at infusion of “750 mg/m² given over a period of ˜2-120 hours to leukemic patients resulted in severe but reversible toxicity.” Ohnuma and Holland, “Initial Clinical Study with Pyrazofurin,” Cancer Treatment Reports, 61(3):389-134 (May/June 1977).

Martelo, et al., reported a dosing regimen of administering pyrazofurin “(150 mg/m² by rapid injection) followed 6 hours later by 5-azacytidine (150 mg/m² by continuous infusion for 5 days).” The authors found that “[i]n this study [pyrazofurin] and [5-azacytidine] appeared to have additive toxic effects on skin and mucous membranes at PF doses >50 mg/m².” Specifically, “[t]his toxicity precluded use of [pyrazofurin] at higher doses, which may be important for enhanced uptake of [5-azacytidine] by leukemic cells exposed to PF.” Martelo, et al., “Phase I Study of Pyrazofurin and 5-Azacytidine in Refractory Adult Acute Leukemia,” Cancer Treat. Rep., 65:237-239 (1981).

Gralla, et al., reporting a dosing regimen of administering pyrazofuring “as a rapid iv injection beginning at a weekly dose of 5 mg/kg (200 mg/m²) with increments of 0.5 mg/kg/week (20 mg/m²) until definite but manageable toxicity occurred.” The dosing was adjusted to 4 mg/kg (160 mg/m²) if the wbc count was 3000-3999/microliter or if the platelet count was 75,000-99,000/microliter.” The authors ultimately found that “[m]ajor therapeutic activity did not occur in the patients entered in this trial” and that pyrazofurin “has little therapeutic value as a single agent in this dose schedule in previously treated patients with advanced lung cancer.” Grallo, et al., “Phase II Evaluation of Pyrazofurin in Patients With Carcinoma of the Lung,” Cancer Treat. Rep., 62(3):451-452 (March 1978).

Example 11: Optimized Dosage Based Metabolite Levels

FIG. 10 is a graph showing the therapeutic benefit of a drug, such as brequinar, that targets a metabolic pathway as a function of levels of a metabolite, such as DHO, that is an intermediate in the pathway. On the left side of the graph, levels of the metabolite are below a minimum threshold, and target engagement of the drug is insufficient to have a therapeutic effect. In the grey region of the graph, levels of the metabolite are above a minimum threshold but below a maximum threshold, so the drug has sufficiently engaged its target to provide a therapeutic effect but has not caused effects that are deleterious to healthy cells. On the right side of the graph, levels of the metabolite are above the maximum threshold, and the effects of the drug cause harm to healthy cells. Adjustments to the dosing regimen based on the relationship between therapeutic benefit and metabolite levels are illustrated in Table 10.

TABLE 10 Metabolite level Adjustment to dosing regimen below minimum threshold increase dosage, frequency of dose of administration, or both above minimum threshold but no change below maximum threshold above maximum threshold decrease dosage, frequency of dose administration, or both

Example 12: Effect of Brequinar-Containing Composition on Patient with AML

The effect of a composition containing brequinar was analyzed on first patient a with acute myeloid leukemia (AML). After administration of a dose of the composition, the patient achieved a DHO plasma level threshold of 1,600 ng/mL in less than 24 hours and remained above that threshold for 84 hours. This patient showed a positive response as indicated by reduction in bone marrow blast count, improvement of extramedullary hematopoiesis, and shift to more differentiation in peripheral blasts.

Example 13: Effect of Brequinar-Containing Composition on Patient with AML

The effect of a composition containing brequinar was analyzed on second patient a with AML. After administration of a dose of the composition, the patient achieved a DHO plasma level threshold of 2,900 ng/mL in less 24 hours and remained above that threshold for 84 hours. This patient showed a positive response to the disease with a lowering of peripheral blasts and increase in absolute neutrophil count, along with greater differentiation of peripheral blasts.

Example 14: Effect of Brequinar-Containing Composition on Patient with AML

The effect of a composition containing brequinar was analyzed on second patient a with AML. After administration of a dose of the composition, the patient achieved a DHO plasma level threshold of 133 ng/mL in less than 2 hours and remained above that threshold for 84 hours. This patient showed a positive response as indicated by a trend towards differentiation of his peripheral blasts.

Example 15

Inhibitors of dihydroorotate dehydrogenase (DHODH), such as brequinar, may be used for the treatment of viral infections, such as SARS-CoV-2 (COVID19) infections. RNA-based viruses require host ribonucleotides for viral replication. Viruses do not have the machinery to synthesize their own ribonucleotides for viral replication and have to use the available intracellular pool of ribonucleotides. Pyrimidines and purines are the building blocks of ribonucleotides for these viruses. Therefore, viral replication can be suppressed by inhibiting synthesis of pyrimidines, purines, or both.

Accordingly, aspects of the invention involve providing one or more agents to inhibit one or more ribonucleotide synthesis pathways in one or more cells, thereby reducing, inhibiting, or suppressing viral replication. In certain embodiments, pyrimidine synthesis is recued, suppressed, and/or inhibited. For example, dihydroorotate dehydrogenase (DHODH) catalyzes the 4th step of de novo pyrimidine synthesis. Inhibition of DHODH prevents the production of uridine monophosphate (UMP). UMP is the building block for thymidine and cytidine nucleotides. There is no bypass pathway to otherwise generate UMP. Inhibition of DHODH results in the depletion of intracellular pyrimidines within hours. Brequinar has been shown to be a potent and orally available inhibitor of DHODH. It is believed that DHODH inhibitors, such as brequinar, effectively suppress viral replication, such as SARS-CoV-2 (COVID19) replication.

In additional or other or combinations of embodiments, inosine monophosphate dehydrogenase (IMPDH) catalyzes the conversion of IMP to XMP, a critical step in the production of guanosine monophosphate (GMP). IMPDH inhibition can suppress the endogenous production of purines when used in combination with a xanthine oxidase inhibitor (e.g. allopurinol) to block a bypass pathway. Mycophenolate mofetil (Cellcept) is an orally available inhibitor of IMPDH with T-cell inhibitory effects marketed as an immunosuppressant medication. Ribavirin is an orally available inhibitor of IMPDH approved for the treatment of Hepatitis C. Ribavirin also has effects on inhibiting cap-dependent translation, which the inventors herein now believe provides antiviral activity. Accordingly, in certain additional, other, or combinations of embodiments, an IMPDH inhibitor may be provided alone or in combination with a DHODH inhibitor in order to, effectively suppress viral replication, such as SARS-CoV-2 (COVID19) replication, by inhibiting both pyrimidine and purine synthesis.

Compositions and dosing regimens for inhibiting ribonucleotide synthesis using, for example DHODH and/or IPDH inhibitors, may be further understood by reference to U.S. Provisional Application Nos. 62/648,320; 62/655,407; 62/533,112, 62/838,514; 62/838,730; 62/859,319; 62/818,186; 62/855,342; 62/916,980; and 62/916,985, PCT International Application Nos. PCT/US2019/064578; PCT/US2019/064586; PCT/US2020/016688; PCT/US2020/016689; and PCT/US2020/021939, PCT International Patent Publication Nos. WO 2019/191032 and WO 2019/191032, U.S. Patent Application Publication Nos. US 2019-0290634; US 2019-0290635; and US 2019-0292154; and U.S. Ser. No. 16/364,423, the contents of each of which is hereby incorporated by reference.

In further aspects of the invention, compositions containing DHODH inhibitors, including brequinar, may be administered for the treatment of viral infections in combination with one or more additional antiviral agents. In certain embodiments, the one or more antiviral agents may be protease inhibitors, RNA dependent RNA polymerase inhibitors, or eIF4E inhibitors.

For example, in some embodiments the DHODH inhibitor may be administered in combination with a protease inhibitor. The protease inhibitor may be one of amprenavir, atazanavir, darunavir, fosamprevanir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, or tipranavir, however it is understood that the protease inhibitor may be any known protease inhibitor. Lopinavir may be provided together with ritonavir as lopinavir/ritonavir.

In other embodiments, the DHODH inhibitor may be administered in combination with an RNA dependent RNA polymerase (RdRp) inhibitor. The RdRp inhibitor may be ribavirin, remdesivir, sofosbuvir, galidesivir, penciclovir, filibuvir, tegobuvir, ponatinib, or favipiravir, however it is understood that the RdRp inhibitor may be any known RdRp inhibitor.

In further embodiments, the DHODH inhibitor may be administered in combination with an eIF4E inhibitor. The eIF4E inhibitor may be hippuristanol, pateamine A, ribavirin, or silverstrol, however it is understood that the eIF4E inhibitor may be any known eIF4E inhibitor. It is further understood that ribavirin is both an eIF4E inhibitor and an IMPDH inhibitor.

Aspects of the present invention encompass combinations of the above inhibitors administered together with a DHODH inhibitor. For example, in embodiments of the invention the DHODH inhibitor may be administered in combination with both a protease inhibitor, such as lopinavir or lopinavir/ritonavir, and an eIF4E inhibitor, such as ribavirin.

The effect of compositions containing DHODH inhibitors, including brequinar, will be analyzed on SARS-CoV-2 (COVID19) positive patients. One cohort of patients will be administered brequinar as 100 mg oral tablet and another cohort will be administered brequinar as a 250 mg oral tablet. After each cohort is administered a DHODH composition, it is believed that each cohort of patients, including the cohorts administered brequinar tablets, will have a positive response to the disease with a lowering of viral replication.

The DHODH inhibitor can be provided alone or in combination with other inhibitors, such as inhibitors that inhibit other nucleotide synthesis pathways. For example, a DHODH inhibitor is an inhibitor that inhibits pyrimidine synthesis. It is envisioned, that methods of the invention may also involve (additionally involve) providing an inhibitor of purine synthesis, thereby inhibits two different ribonucleotide synthesis pathways. In such embodiments, the effect of compositions of DHODH inhibitors in combination with inosine-5′-monophosphate dehydrogenase (IMPDH) inhibitors, including ribavirin, mycophenolate mofetil, and allopurinol, will be tested on SARS-CoV-2 (COVID19) positive patients. After administration of each combination, it is believed that these patients will also show a positive response to the disease with a lowering of viral replication.

In aspects of the invention, the DHODH inhibitor can be provided in combination with one or more antiviral compounds. For example, the DHODH inhibitor is an inhibitor that inhibits pyrimidine synthesis. It is envisioned, that methods of the invention may also involve (additionally involve) providing one or more antiviral agents that inhibit a pathway. In such embodiments, the effect of compositions of DHODH inhibitors in combination with one or more protease inhibitors, RNA dependent RNA polymerase inhibitors, and eIF4E inhibitors, including lopinavir/ritonavir, ribavirin, and remdesivir, will be tested on SARS-CoV-2 (COVID19) positive patients. For example, the effect of the DHODH inhibitor can be tested in combination with ribavirin, in combination with remdesivir, in combination of favipiravir, in combination with lopinavir/ritonavir, or in combination with both ribavirin and lopinavir/ritonavir. After administration of each combination, it is believed that these patients will also show a positive response to the disease.

The effect of combinations including brequinar plus ribavirin or brequinar plus mycophenolate mofetil can then be tested for use as an emergency treatment of SARS-CoV-2 (COVID19) positive patients. Patients can be administered compositions containing brequinar according to the following dosing regimens:

Regimen 1: brequinar+ribavirin

-   -   brequinar 2-doses given 3-days apart (Q3D)         -   Dose: <50 kg: 250 mg, 50-75 kg: 350 mg, >75 kg: 500 mg     -   ribavirin 400 mg twice daily (bid)×14-doses         Regimen 2: brequinar+mycophenolate     -   brequinar 2-doses given 3-days apart (Q3D)         -   Dose: <50 kg: 250 mg, 50-75 kg: 350 mg, >75 kg: 500 mg     -   mycophenolate 1000 mg twice daily (bid)×14-doses         Regimen 3: brequinar+mycophenolate+allopurinol     -   brequinar 2-doses given 3-days apart (Q3D)         -   Dose: <50 kg: 250 mg, 50-75 kg: 350 mg, >75 kg: 500 mg     -   mycophenolate 1000 mg twice daily (bid)×14-doses     -   allopurinol 300 mg daily×7-doses         Regimen 4: leflunomide+mycophenolate+allopurinol     -   leflunomide 100 mg daily×5-doses     -   mycophenolate 1000 mg twice daily (bid)×14-doses     -   allopurinol 300 mg daily×7-doses

The skilled artisan will appreciate that different combinations and different dosing amounts are within the scope of the invention, and the above combinations and doses are exemplary and non-limiting doses and combination.

After administration, it is believed that viral replication will be suppressed.

Example 16

Several aspects of brequinar make it useful for treating viral infections. For example, Brequinar was assayed against the rhinovirus.

Brequinar was solubilized at 10 mM in sterile water immediately prior to assay set up. Test material was evaluated using a high-test concentration of 10 μM and eleven serial two-fold dilutions for the antiviral assay. Brequinar was diluted to 20 μM (2× starting concentration; 2.6 μL of 10 mM stock) in drug dilution tubes containing 1297.4 μL of assay medium. Six hundred fifty microliters (650 μL) of the 20 μM solution was transferred to 650 μL of assay medium (two=fold dilution) for a total of eleven serial dilutions. One hundred microliters (100 μL) of each 2× test concentration were added in triplicate wells for efficacy, duplicate wells for cytotoxicity, and a single well per concentration for colorimetric evaluation. Rupintrivir (HEV) as sold by MedChem Express (Monmouth Junction, N.J.) was evaluated as a positive control compound in the antiviral assay.

H1-HeLa cells (CRL-1958) were passaged in the medium sold under the trade name Dulbecco's Modified Eagle Medium (DMEM) by Gibco with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin in T-75 flasks prior to use in the antiviral assay. On the day preceding the assay, the cells were split 1:2 to assure they were in an exponential growth phase at the time of infection. Total cell and viability quantification was performed using a hemocytometer and Trypan Blue dye exclusion. Cell viability was greater than 95% for the cells to be utilized in the assay. The cells were resuspended at 2×104 cells per well in tissue culture medium and added to flat bottom microtiter plates in a volume of 100 μL. The plates were incubated at 37° C./5% CO2 overnight to allow for cell adherence. The cells were approximately 90% confluent following the overnight incubation.

Each plate contained cell control wells (cells only), virus control wells (cells plus virus), drug toxicity wells (cells plus drug only), drug colorimetric control wells (drug only) as well as experimental wells (drug plus cells plus virus). Brequinar was tested in triplicate wells for efficacy, duplicate wells for cytotoxicity and a single colorimetric control well per twelve test concentrations of compound. Compound was added to the cell monolayers immediately prior to infection at 100 μL per well. Rupintrivir was evaluated as a positive control compound at six test concentrations.

HRV1A strain 2060 was grown in H1-HeLa cells for the production of stock virus pools. An aliquot of virus was removed from the freezer (−80° C.) and allowed to thaw slowly to room temperature in a biological safety cabinet. Virus was diluted into assay medium (DMEM supplemented with 2% heat-inactivated FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin) such that the amount of virus added to each well in a volume of 100 μL was the amount determined to yield 85 to 95% cell killing at 3 days' post-infection.

Following incubation at 37° C. in a 5% CO2 incubator for three days, the test plates were stained with the tetrazolium dye XTT (2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)carbonyl]-2H-tetrazolium hydroxide). XTT-tetrazolium was metabolized by the mitochondrial enzymes of metabolically active cells to a soluble formazan product, allowing rapid quantitative analysis of the inhibition of virus-induced cell killing by antiviral test substances. XTT solution was prepared daily as a stock of 1 mg/ml in RPM11640. Phenazine methosulfate (PMS) solution was prepared at 0.15 mg/ml in PBS and stored in the dark at −20° C. XTT/PMS stock was prepared immediately before use by adding 40 μL of PMS per ml of XTT solution. Fifty microliters (50 μL) of XTT/PMS were added to each well of the plate and the plate was reincubated for 4 hours at 37° C. Plates were sealed with adhesive plate sealers and shaken gently or inverted several times to mix the soluble formazan product and the plate was read spectrophotometrically at 450/650 nm with a Molecular Devices Vmax plate reader.

Table 12 summarizes the in vitro antiviral activity of brequinar and Rupintrivir.

TABLE 11 H1-HeLa/HRV1A₂₀₆₀ COMPOUND EC50 (μM) TC50 (μM) Therapeutic Index Rupintrivir (nM) 10.7 >100 >9.35 Brequinar 0.05 0.30 6.00

Example 17

Several aspects of brequinar make it useful for treating SARS-CoV-2 infections. First, SARS-CoV-2 has an overwhelming reliance on host nucleotides, and >50% of total RNA transcripts in infected cells are viral mRNA. In addition, brequinar can be given orally and daily at safe and effective doses, and inhibition of DHODH will deny SARS-CoV-2 the nucleotides it needs for viral replication. Finally, brequinar targets the host, rather than the virus, so it will not promote the development of resistance and will not be neutralized by the viral mutations that can compromise the efficacy of direct-acting antivirals.

FIG. 11 is a schematic showing the role of DHODH in pyrimidine synthesis. DHODH converts dihydroorotate to orotate.

Without wishing to be bound by a particular theory or mechanism of action, the following are mechanisms by which brequinar may treat infection with SARS-CoV-2. First, brequinar may block viral replication by inhibiting de novo pyrimidine synthesis. RNA-based viruses, such as SARS-CoV-2, do not have the machinery to supply their own ribonucleotides, so they must steal from the pool of host nucleotides for intracellular replication of their viral genomes. Additionally or alternatively, brequinar may attenuate the autoimmune response. Acute respiratory distress syndrome in COVID-19 patients is believed to be caused by cytokine storm, the excessive release of cytokines by the innate immune system. DHODH is a known and effective target in autoimmune disease, suppressing overactive T-cell response and dysregulated cytokine production. Leflunomide and teriflunomide are DHODH inhibitors approved for rheumatoid arthritis and multiple sclerosis but are not sufficiently potent to treat COVID-19. However, brequinar is 500× more potent than those DHODH inhibitors.

Table 12 summarizes the in vitro antiviral activity of brequinar toward various viruses.

TABLE 12 EC₅₀ CC₅₀ Organism Cell line (μM) (μM) SI Dengue¹ A549 (human alveolar basal 0.078 >5 >64 epithelial) Zika² Vero76 (monkey kidney) 0.08 >50 >625 Respiratory Syncytial A549 or HEp-2 (human 0.053 >10 >189 (RSV)³ epithelial) HIV1⁴ TZM-bl(human cervical tumor) 0.04 >30 >750 Influenza A MDCK (canine kidney) 0.78, 0.62, 0.25 >50 >64, >80, >200 H1N1(California), H3N2, Influenza B (Brisbane)⁵ Influenza A MDCK (canine kidney) 0.58 >50 >86 H1N1(BIRFLU)⁵ Influenza A A549 (human alveolar basal 0.14 >50 >357 H1N1(BIRFLU)⁵ epithelial) Influenza A H1N1 (New 16HBE (human bronchial 0.14 >50 >357 Caledonia)⁵ epithelial) Ebola⁶ HeLa (human cervical tumor) 0.1 >25 >250 Yellow Fever⁷ Vero (monkey kidney) 0.02 >50 >2500 VSV⁷ HuH7 (human hepatocellular 0.014 >25 >1785 carcinoma) FMDV IBRS-2 (swine kidney) 30 100 3 (O/MY98/BY/2010)⁸ FMDV IBRS-2 (swine kidney) <3 100 >33 (A/GD/MM/2013)⁸ CMV⁹ Primary Human Fibroblasts 0.8 >50 >62 SARS-CoV-2 Vero E6 (monkey kidney) 0.197 >50 >250 ¹Qing M et al. Antimicrobial Agents and Chemotherapy. 2010; 54(9)3686-3695 ²Adcock, R. S. et al. Antiviral Res 2017. 138: 47-56 ³Bonavia, A. et al. PNAS 2011. 108: 17, 6739 ⁴Andersen et al, Viruses, 2019 11, 964. ⁵Park et al. J of Virology 2020. Vol 94; 7 e02149-19 ⁶Luthra et al. Antiviral Res 2018. 158: 288-302 ⁷Tan et al. (2005) U.S. Pat. No. 6,841,561 ⁸Li et al. Biomed Pharmacother 2019. 116: 108982 ⁹Marschall et al. Antiviral Res. 2013. 100: 640-648

FIG. 12 is graph of the percentage maximum effect of brequinar toward SARS-CoV-2 as a function of brequinar concentration. Vero E6 cells were infected at a multiplicity of infection (MOI) of 0.05. Brequinar's EC₉₀ is 0.345 μM. In rodents, brequinar has a lung penetrance of about 50%, and the target brequinar concentration is at least 0.7 μM. The results show that brequinar is highly potent against SARS-CoV-2.

FIG. 13 is a graph of the IC₅₀ of remdesivir toward SARS-CoV-2 as a function of brequinar concentration. Vero E6 cells were infected at a multiplicity of infection MOI of 0.05. In addition, brequinar lowers the EC₅₀ of remdesivir more >40-fold. The results show that a combination of brequinar and remdesivir is highly potent against SARS-CoV-2 in vitro and suggest that a combination of the two drugs may have excellent therapeutic potential.

The following attributes make brequinar advantageous for treatment of COVID-19:

-   -   Suitable for treatment for all stages of COVID-19 stages in         conjunction with the standard of care     -   Acceptable for daily administration     -   Can be administered orally or intravenously, and oral and IV         formulations are equivalent     -   >90% bioavailability when administered orally     -   No cumulative effective of repeated doses     -   Does not inhibit CYP     -   Predictable pharmacokinetics across 31 clinical studies     -   Proven safety: 46 subjects have already been evaluated at the         proposed dose and schedule

The efficacy of brequinar in treating COVID-19 is evaluated according in a clinical trial as follows. Twenty-four patients are enrolled in a randomized, controlled study. Patients meet the following selection criteria: hospitalized but not in intensive care unit; within 10 days of first COVID-19 symptoms; and at least one high risk factor, such as hypertension, diabetes, chronic kidney disease, chronic obstructive pulmonary disease, asthma, cardiovascular disease, liver cirrhosis, over 65 years of age, and body mass index over 30. Sixteen patients are given standard-of-care plus brequinar, 100 mg/day administered orally once per day, and eight are given standard-of-care alone. The following efficacy endpoints are analyzed: status or duration of hospitalization; National Early Warning Score 2 (NEWS2); mortality through day 29; changes in viral load to day 15; and changes in inflammatory markers to day 15

The dosage 100 mg/day brequinar administered orally once per day is selected based on a series of findings. First, the pharmacokinetics of comparable doses of intravenously administered brequinar are well-characterized. When brequinar is given at 100 mg/day×5 days, the trough level in the plasm is 2 μM. In addition, brequinar is 90% orally bioavailable, and the lung penetrance of brequinar in rodents is ˜50%, so a dosage of 100 mg/day orally is expected to achieve a concentration of approximately 1 μM in the lungs. DHODH is almost completely inhibited at concentrations >1 μM, and a lung concentration of 1 μM is >>EC₉₀ of 0.345 μM.

FIG. 14 is a graph of brequinar concentration in the plasma of a patient during a 5-day course of once-per-day doses. 106 mg brequinar was administered intravenously in a single daily dose for 5 days. The dotted red line shows that the brequinar concentration remained at or above 0.75 μg/mL, equivalent to 2 μM, throughout the duration of the study.

The effects of brequinar on engraftment of human tumors in mice were analyzed. Mice were injected subcutaneously with MV411 tumor cells and treated with brequinar and ribavirin, either alone or in combination. In both individual and combination therapies, brequinar was dosed orally every three days at 50 mg/kg. In both individual and combination therapies, ribavirin was dosed orally daily at either 50 mg/kg or 100 mg/kg. Tumor size was measured twice per week.

FIG. 15 is graph of tumor size in mice treated with brequinar alone, ribavirin alone, or brequinar and ribavirin in combination. Drugs were given at dosages indicated.

FIG. 16 is graph of tumor size in mice treated with 50 mg/kg brequinar and 100 mg/kg ribavirin.

FIG. 17 is graph of tumor size in mice treated with 50 mg/kg brequinar and 50 mg/kg ribavirin.

The result shows that combination therapies including brequinar and ribavirin are more effective at suppressing tumor growth than are therapies that include either drug individually.

Example 18

Objective

Brequinar is a potent pyrimidine synthesis inhibitor with anti-cancer effects as well as antiviral effects. Brequinar's primary antiviral mechanism is believed to be via the depletion of the intracellular pyrimidine nucleotide pool.

RNA viruses require a massive amount of ribonucleotides for replication within infected cells. The inhibition of pyrimidine synthesis and depletion of these ribonucleotides would be expected to decrease viral replication by starving the virus of its pyrimidine building blocks. The synthesis of SARS-CoV-2 viral RNA in infected cells dominates total RNA synthesis within the cell; the viral RNA can make up >50% of total RNA, confirming the high demand on the host pyrimidine and purine biosynthesis for successful viral replication.

Based on these premises, the anti-SARS-CoV-2 effect of brequinar was evaluated in an in vitro model. Further, brequinar was evaluated in combination with clinically available drugs to determine whether it can potentiate their activity against SARS-CoV2 with the goal of increasing efficacy and potentially reducing the duration of required treatment.

Methods

Cells and Viruses

Vero E6 cells (ATCC) were cultured and maintained in Dulbecco's Modified Essential Media (DMEM) supplemented with 10% FBS in a 37° C. incubator with 5% CO2. SARS-CoV-2 was obtained from BEI resources.

Dose-Response Studies

Antiviral activity was measured with the CPE-protection assay. Vero E6 cells were seeded into white well plates at a cell density of 15,000 cells per well in a volume of 45 μL and incubated in an actively humidified incubator with 5.0% CO2 at 37° C. and 95% humidity for 48 hours. Test compounds diluted in 30 μL of cell culture media were added to each well, and the final DMSO concentration was kept at 0.25%. After a two-hour incubation at 37° C. with 5% CO2, a 750 pfu (or MOI of 0.05) of virus (or cell culture media for cytotoxicity assay) was added to the wells in a volume of 15 μL; then, the plates were incubated for three days in an actively-humidified incubator with 5% CO2 at 37° C. and 95% humidity. The cell viability was measured with 90 μL per well of CellTiter-Glo reagent (Promega). The dose-response studies used concentrations from 5 to 0.039 μM by 2-fold dilution with triplicates for each point. For combinatorial tests, 8 different concentrations of brequinar were tested in a dose-response assay. Dose response curves and analyses were performed with XLFit (IDBS).

Test Articles

Brequinar was provided by Clear Creek Bio (MA, USA) and other compounds were purchased from CSNpharm (IL, USA).

Results

Potency and Cytotoxicity of Anti-SARS-CoV-2 Activity of Brequinar

The anti-SARS-CoV-2 activity of brequinar was evaluated and compared to other compounds. Results are provided in Table 13.

TABLE 13 Antiviral activity IC₅₀ EC₅₀ EC₉₀ CC₅₀ Compound (μM)* (μM)** (μM)** E_((Max))** (μM) SI₅₀*** brequinar 0.200 0.197 0.345 88.2 >50 >250 remdesivir 0.820 0.820 1.400 100 >50 >61 ribavirin >50 >50 >50 NA >50 NA GC-376 2.044 2.044 5.73 100 >50 >24.5 *IC₅₀: Concentration inhibiting 50% of the virus-induced CPE compared to the no infection control. **EC₅₀ and EC₉₀: Concentration inhibiting 50% of the maximum CPE-protection effect of the compound (E_(max)) ***SI₅₀: Selective Index 50 = CC₅₀/IC₅₀

Brequinar demonstrated an IC₅₀ of 0.2 μM, indicating potent antiviral activity. While the antiviral potency of brequinar was the highest among the test compounds, its maximal inhibitory activity (E_(ma)) was 88.2% when compared to the no infection control; this differed from the E_(max) of remdesivir and GC-376 (a SARS-CoV protease inhibitor).

FIG. 18 is a graph of percentage maximal effect of brequinar as a function of brequinar concentration. The results show that brequinar has an EC₅₀ of about 0.2 μM and an EC₉₀ of 0.345 μM.

Brequinar Potentiates the Antiviral Effect of Remdesivir

To test whether brequinar could potentiate the antiviral effect of remdesivir against SARS-CoV-2, the two compounds were assayed across a range of concentrations. The results are summarized in Table 14.

TABLE 14 Dose response antiviral activity of remdesivir brequinar IC₅₀ EC₅₀ Max Data Min Data CC₅₀ (μM) (μM) (μM) E(Max) (%) (%) (μM) 0.000 0.823 0.801 92.02 97.1 −11 >25 0.078 0.292 0.277 97.37 94.4 −1.9 >50 0.156 0.102 0.186 122.66 102.6 22.1 >50 0.313 0.003* 0.003* 97.35 103.8 55.4 >50 0.625 <0.0195 <0.0195 95.33 104.7 75.9 >50 1.250 <0.0195 <0.0195 100.22 105.1 80.1 >50 2.500 <0.0195 <0.0195 96.37 106.8 78.9 >50 5.000 <0.0195 <0.0195 95.10 101.9 69.5 >50 *Extrapolated values

FIG. 19 is graph showing the effect of brequinar on the anti-SARS-CoV-2 efficacy of remdesivir. Each drug was given at the concentration indicated in the graph. Values are indicated relative to non-infected control.

The results show that addition of brequinar greatly potentiated antiviral effects of remdesivir and this effect was evident when brequinar was added at a concentration lower than its IC₅₀. For example, while the single treatment of remdesivir required 0.823 μM to suppress viral replication to 50%, the same degree of inhibition was achieved by 0.1 μM of remdesivir when it was co-treated with 0.16 μM of brequinar, indicating a >6.8-fold increase in activity. In the presence of brequinar at concentrations greater than 0.31 μM (which is greater than the IC₅₀ of brequinar), all of tested wells demonstrated between 70% and 100% suppression of viral replication, possibly due to the antiviral effect of brequinar. No enhanced cytotoxicity was detected by the co-treatment.

CONCLUSION

These experiments indicate that brequinar has potent anti-SARS-CoV-2 activity with an EC₅₀ of ˜200 nM. The EC₅₀ of ˜200 nM is much lower than its cytotoxic concentration. Brequinar potentiates the antiviral of remdesivir at concentrations down to ˜160 nM. The benefit of brequinar co-treatment may be due to the potentiation of remdesivir activity at lower brequinar concentrations as well as combined direct antiviral activity by nucleotide depletion at higher concentrations.

Example 19

The mechanism by which administration of a DHODH inhibitor according to a daily dosing regimen inhibits viral replication is illustrated below. The DHODH inhibitor brequinar is administered once per day for five consecutive days to a subject infected with an RNA virus. Throughout the course of the dosing regimen, levels of intracellular pyrimidines, such as uridine, and viral replication are measured.

FIG. 20 is a graph showing the levels of brequinar in the plasma of a subject that receives a single daily dose of brequinar for five consecutive days.

FIG. 21 is a graph showing both the levels of intracellular pyrimidines and the levels of brequinar in the plasma of a subject that receives a single daily dose of brequinar for five consecutive days. Pyrimidine levels are shown in green, and brequinar levels are shown in grey. The first peak in brequinar level corresponds to a dramatic decrease in the intracellular pyrimidine pool. Thereafter, intracellular pyrimidine levels fluctuate slightly as brequinar levels wax and wane, but they consistently remain well below the starting level throughout the course of the dosing regimen.

FIG. 22 is a graph showing both the levels of viral replication and the levels of brequinar in the plasma of a subject that receives a single daily dose of brequinar for five consecutive days. Viral replication is shown in teal, and brequinar levels are shown in grey. The first peak in brequinar level corresponds to a dramatic reduction in viral replication due to the decrease in intracellular pyrimidine pools. Thereafter, although brequinar levels wax and wane, viral replication remains consistently low due the sustained decrease in intracellular pyrimidine pools.

Taken together, these results show that a DHODH inhibitor, such as brequinar, is effective for treating viral infections. Viral replication requires an adequate supply of intracellular nucleotides, such as pyrimidines, and DHODH inhibitors limit pyrimidine availability. When administered according to an appropriate dosing regimen, a DHODH inhibitor triggers a sustained decrease in nucleotide supply despite wide variations in levels of the drug itself over the course of the regimen. The decrease in intracellular nucleotide pools is sustained for a period long enough to prevent viral replication, but it may be followed by a drug-free period that allows partial or complete restoration of nucleotide supply as needed to support normal cellular homeostatic functions.

INCORPORATION BY REFERENCE

References and citations to other documents, such as patents, patent applications, patent publications, journals, books, papers, web contents, have been made throughout this disclosure. All such documents are hereby incorporated herein by reference in their entirety for all purposes.

EQUIVALENTS

Various modifications of the invention and many further embodiments thereof, in addition to those shown and described herein, will become apparent to those skilled in the art from the full contents of this document, including references to the scientific and patent literature cited herein. The subject matter herein contains important information, exemplification, and guidance that can be adapted to the practice of this invention in its various embodiments and equivalents thereof. 

What is claimed is:
 1. A method of treating a viral infection in a subject, the method comprising providing to a subject having a viral infection an agent that inhibits a nucleotide synthesis pathway in cells of the subject, thereby reducing, suppressing, or inhibiting viral replication.
 2. The method of claim 1, wherein the viral infection is a respiratory viral infection.
 3. The method of claim 2, wherein the respiratory viral infection comprises a virus selected from the group consisting of an adenovirus, coronavirus, human metapneumovirus, human parainfluenza virus, human respiratory syncytial virus, influenza virus, and rhinovirus.
 4. The method of claim 3, wherein the virus is a coronavirus selected from the group consisting of Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
 5. The method of claim 4, wherein the coronavirus is SARS-CoV-2.
 6. The method of claim 1, wherein the agent inhibits pyrimidine synthesis.
 7. The method of claim 6, wherein the agent is a dihydroorotate dehydrogenase (DHODH) inhibitor.
 8. The method of claim 7, wherein the DHODH inhibitor is selected from the group consisting of brequinar, a brequinar analog, a brequinar derivative, a brequinar prodrug, a micellar formulation of brequinar, and a brequinar salt.
 9. The method of claim 8, wherein the brequinar salt is a sodium salt.
 10. The method of claim 6, further comprising providing to the subject an antiviral agent.
 11. The method of claim 10, wherein the antiviral agent is selected from the group consisting of a 3C-like main protease inhibitor, eIF4E inhibitor, helicase inhibitor, inhibitor or a viral protein that binds to a host receptor, inhibitor of a viral structural protein, inhibitor of a virulence factor, inosine monophosphate dehydrogenase (IMPDH) inhibitor, interferon, papain-like proteinase inhibitor, protease inhibitor, RNA-dependent RNA polymerase inhibitor, and xanthine oxidase inhibitor.
 12. The method of claim 11, wherein the antiviral agent is a protease inhibitor,
 13. The method of claim 12, wherein the protease inhibitor is lopinavir.
 14. The method of claim 10, wherein the antiviral agent is an RNA-dependent RNA polymerase inhibitor.
 15. The method of claim 14, wherein the RNA-dependent RNA polymerase inhibitor is selected from the group consisting of remdesivir and favipiravir.
 16. The method of claim 10, wherein the antiviral agent is an eIF4E inhibitor.
 17. The method of claim 16, wherein the eIF4E inhibitor is ribavirin.
 18. The method of claim 6, further comprising providing to the subject an agent that inhibits purine synthesis.
 19. The method of claim 18, wherein the agent that inhibits purine synthesis is an inosine monophosphate dehydrogenase (IMPDH) inhibitor.
 20. The method of claim 19, wherein the IMPDH inhibitor is selected from the group consisting of ribavirin and mycophenolate mofetil.
 21. The method of claim 1, wherein the agent that inhibits a nucleotide synthesis pathway is provided orally or intravenously. 